Andrew Godoski sees allusions to Christ, including Neo's "virgin birth", his doubt in himself, the prophecy of his coming, along with many other Christian references.[35] Amongst these possible allusions, it is suggested that the name of the character Trinity refers to Christianity's doctrine of the Trinity.[159] It has also been noted that the character Morpheus paraphrases the Chinese taoist philosopher Zhuangzi when he asks Neo, "Have you ever had a dream, Neo, that you were so sure was real? What if you were unable to wake from that dream? How would you know the difference from the real world and the dream world?"[160]

Matrixism is a fan-based possibly satirical religion created as "the matrix religion".

Philosopher William Irwin suggests that the idea of the "Matrix" – a generated reality invented by malicious machines – is an allusion to Descartes' "First Meditation", and his idea of an evil demon. The Meditation hypothesizes that the perceived world might be a comprehensive illusion created to deceive us.[157] The same premise can be found in Hilary Putnam's brain in a vat scenario proposed in the 1980s.[157] A connection between the premise of The Matrix and Plato's Allegory of the Cave has also been suggested. The allegory is related to Plato's theory of Forms, which holds that the true essence of an object is not what we perceive with our senses, but rather its quality, and that most people perceive only the shadow of the object and are thus limited to false perception.[35]

The philosophy of Immanuel Kant has also been claimed as another influence on the film, and in particular how individuals within the Matrix interact with one another and with the system. Kant states in his Critique of Pure Reason that people come to know and explore our world through synthetic means (language, etc.), and thus this makes it rather difficult to discern truth from falsely perceived views. This means people are their own agents of deceit, and so in order for them to know truth, they must choose to openly pursue truth. This idea can be examined in Agent Smith's monologue about the first version of the Matrix, which was designed as a human utopia, a perfect world without suffering and with total happiness. Agent Smith explains that, "it was a disaster. No one accepted the program. Entire crops [of people] were lost." The machines had to amend their choice of programming in order to make people subservient to them, and so they conceived the Matrix in the image of the world in 1999. The world in 1999 was far from a utopia, but still humans accepted this over the suffering-less utopia. According to William Irwin this is Kantian, because the machines wished to impose a perfect world on humans in an attempt to keep people content, so that they would remain completely submissive to the machines, both consciously and subconsciously, but humans were not easy to make content.[158]

In The Matrix, a copy of Jean Baudrillard's philosophical work Simulacra and Simulation, which was published in French in 1981, is visible on-screen as "the book used to conceal disks",[7][40] and Morpheus quotes the phrase "desert of the real" from it.[144] "The book was required reading"[7] for the actors prior to filming.[40][145] However, Baudrillard himself said that The Matrix misunderstands and distorts his work.[144][146] Some interpreters of The Matrix mention Baudrillard's philosophy to support their claim "that the [film] is an allegory for contemporary experience in a heavily commercialized, media-driven society, especially in developed countries".[7] "The influence of [Baudrillard] was brought to the public's attention through the writings of art historians such as Griselda Pollock and film theorists such as Heinz-Peter Schwerfel".[7] In addition to Baudrillard, the Wachowskis were also significantly influenced by Kevin Kelly's Out of Control: The New Biology of Machines, Social Systems, and the Economic World, and Dylan Evans’s ideas on evolutionary psychology.[16] The film makes several references to Lewis Carroll's Alice's Adventures in Wonderland.[110] Comparisons have also been made to Grant Morrison's comic series The Invisibles, with Morrison describing it in 2011 as "(it) seemed to me (to be) my own combination of ideas enacted on the screen".[147] Comparisons have also been made between The Matrix and the books of Carlos Castaneda.[148]

The Matrix belongs to the cyberpunk genre of science fiction, and draws from earlier works in the genre such as the 1984 novel Neuromancer by William Gibson.[8] For example, the film's use of the term "Matrix" is adopted from Gibson's novel,[149] though L. P. Davies had already used the term "Matrix" fifteen years earlier for a similar concept in his 1969 novel The White Room ("It had been tried in the States some years earlier, but their 'matrix' as they called it hadn't been strong enough to hold the fictional character in place").[150] After watching The Matrix, Gibson commented that the way that the film's creators had drawn from existing cyberpunk works was "exactly the kind of creative cultural osmosis" he had relied upon in his own writing;[8] however, he noted that the film's Gnostic themes distinguished it from Neuromancer, and believed that The Matrix was thematically closer to the work of science fiction author Philip K. Dick, particularly Dick's speculative Exegesis.[8] Other writers have also commented on the similarities between The Matrix and Dick's work;[138][151][152] one example of such influence is a Philip K. Dick's 1977 conference, in which he stated: "We are living in a computer-programmed reality, and the only clue we have to it is when some variable is changed, and some alteration in our reality occurs".[153][154][155][156]

The pods in which the machines keep humans have been compared to images in Metropolis, and the work of M. C. Escher.[126] A resemblance to the eery worlds of Swiss artist H.R. Giger was also recognized.[127][128] The pods can be seen in Welcome to Paradox Episode 4 "News from D Street" from a 1986 short story[129] of the same name by Andrew Weiner which aired on September 7, 1998, on the SYFY Channel and has a remarkably similar concept. In this episode the hero is unaware he is living in virtual reality until he is told so by "the code man" who created the simulation and enters it knowingly. The Wachowskis have described Stanley Kubrick's 2001: A Space Odyssey as a formative cinematic influence, and as a major inspiration on the visual style they aimed for when making The Matrix.[130][131][132] Rainer Werner Fassbinders German TV Miniseries World on a Wire from 1973, an adaption of the novel Simulacron-3, served as inspirational source for some details of The Matrix, such as the transfer between the real world and the Matrix-simulation via telephone / phonebooth.[citation needed] Reviewers have also commented on similarities between The Matrix and other late-1990s films such as Strange Days, Dark City, and The Truman Show.[105][133][134][135][136] The similarity of the film's central concept to a device in the long-running series Doctor Who has also been noted. As in the film, the Matrix of that series (introduced in the 1976 serial The Deadly Assassin) is a massive computer system which one enters using a device connecting to the head, allowing users to see representations of the real world and change its laws of physics; but if killed there, they will die in reality.[137] The action scenes of The Matrix were also strongly influenced by live-action films such as those of director John Woo.[138] The martial arts sequences were inspired by Fist of Legend, a critically acclaimed 1995 martial arts film starring Jet Li. The fight scenes in Fist of Legend led to the hiring of Yuen as fight choreographer.[139][140]

The Wachowskis' approach to action scenes drew upon their admiration for Japanese animation such as Ninja Scroll and Akira.[9] Director Mamoru Oshii's 1995 animated film Ghost in the Shell was a particularly strong influence;[9] producer Joel Silver has stated that the Wachowskis first described their intentions for The Matrix by showing him that anime and saying, "We wanna do that for real".[141][142] Mitsuhisa Ishikawa of Production I.G, which produced Ghost in the Shell, noted that the anime's high-quality visuals were a strong source of inspiration for the Wachowskis. He also commented, "... cyberpunk films are very difficult to describe to a third person. I'd imagine that The Matrix is the kind of film that was very difficult to draw up a written proposal for to take to film studios". He stated that since Ghost in the Shell had gained recognition in America, the Wachowskis used it as a "promotional tool".[143]