The Matrix makes numerous references to recent films and literature, and to historical myths and philosophy including Messianism, Buddhism, Gnosticism, Existentialism, Nihilism, Vedanta, Advaita Hinduism, Yoga Vashishta Hinduism and Sikhism. The film's premise resembles Plato's Allegory of the cave, René Descartes's evil genius, Kant's reflections on the Phenomenon versus the Ding an sich, and the brain in a vat thought experiment, while Jean Baudrillard's Simulacra and Simulation is featured in the film. Bracha L. Ettinger's "Matrix" Notebooks from the 1980s and Matrixial theory from the 1990s are considered by art historians a significant influence on the film. There are similarities to cyberpunk works such as Neuromancer by William Gibson.

Neo is an anagram of "One", significant because of the main character's journey and eventual realization of self.

Japanese director Mamoru Oshii's Ghost in the Shell was a strong influence. Producer Joel Silver has stated that the Wachowski brothers first described their intentions for The Matrix by showing him that anime and saying, "We wanna do that for real". 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 Wachowski brothers. 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 Wachowski brothers used it as a "promotional tool".

The whole Matrix series can also be interpreted as the story of Jesus, with Neo, Trinity and Morpheus representing the Holy Trinity. Neo represents Jesus (the Son), Trinity represents the Holy Spirit and Morpheus represents the Father. Neo also has extraordinary powers and dies before being brought back to life. Adding credence to this idea is the fact that "Anderson" means "Son of Man."