A Wrinkle in Time is a book about the battle between good and evil and the ultimate triumph of love. Every character is clearly identified with either good or evil: the "good" characters include Meg, her family, Calvin, the Mrs. W's, Aunt Beast, and the Happy Medium; the "evil" characters include IT, The Dark Thing, and the Man with the Red Eyes. In the absence of any ambiguities or shades of gray, the book's central conflict is clearly and starkly dramatized so that readers of all ages can understand its themes and its message.

Many of the book's central messages are contained in the lessons of life that Meg must learn in order to successfully complete her quest. First, she must learn to overcome her desire for conformity and appreciate her own uniqueness as an individual. In the beginning of the book, Meg feels awkward and out of place at her high school. She is involved in frequent fights with her peers and is sent to the principal's office for her misbehavior. Meg tells her mother that she hates being so different and wishes she could just pretend she was like everyone else. This wish comes terribly true in the form of Camazotz, with its rows of identical houses and identical human beings; the planet is a parody of her extreme desire for conformity. Only after she recognizes the evil of this planet does she appreciate the value of being an individual. Outside of this specific plotline, the book also more generally celebrates human creativity and individuality, hailing as heroes the greatest creative geniuses in the arts and sciences, including Einstein, Bach, da Vinci, and Shakespeare.

Another important lesson that Meg must learn is that she cannot know everything. In the beginning of the book, Meg insists that nothing remain unexplained or unquantified. For example, when she meets Calvin, she immediately asks her mother what she thinks of him; she wants an instant and definitive answer. Her mother urges her to be patient, but Meg cannot wait for opinions to form gradually. Meg wants to comprehend everything around her all at once. However, in the course of her travels, she slowly comes to appreciate her mother's words of wisdom: "Just because we don't understand doesn't mean an explanation doesn't exist." She can accept that the musical dance of the creatures on Uriel is beautiful even though she cannot speak their language; she can accept that the Black Thing is evil even though she does not really understand what it is. When she ultimately confronts IT on her return visit to Camazotz, she can at last appreciate the dangers of a mind bent on total understanding, on definitive and authoritative explanations: such a mind becomes robot-like, mechanical, and unfeeling. Meg's rejection of IT is thus also a rejection of the need for total understanding of the world around her.

Yet another theme of the book and an important lesson for Meg is the inadequacy of words. Author L'Engle transports her characters to several other planets on which communication takes place through some means other than language. Mrs. Who explains that it is very difficult for her to verbalize her thoughts, and thus she usually resorts to quotation; Aunt Beast tells Meg that "it is not easy at all to put things the way your mind shapes them." The beasts normally communicate through their tentacles, just like the creatures on Uriel make music by moving their great wings. Charles Wallace can communicate with Meg by reading her mind. L'Engle thus demonstrates that verbal speech is not the only way in which we can share our thoughts and feelings. Meg learns this lesson in her rescue of Charles Wallace: she ultimately triumphs over IT not through eloquent pleas or persuasive rhetoric, but through the sheer power of a love too great for words.

The triumph of love is one of several allusions in the novel to Christian theology. Jesus is the first figure cited by Mrs. Whatsit as a fighter against the Dark Thing. Indeed, the whole imagery of light vs. darkness is traced back to the New Testament by Mrs. Who in her fondness for quotation: "And the light shineth in darkness; and the darkness comprehended it not." In addition, Mrs. Whatsit translates the musical dance of the creatures on Uriel into the Biblical words of the prophet Isaiah, and Mrs. Who's second gift to Meg is an excerpt from St. Paul's Epistle to the Corinthians. Yet the characters are never identified as Christians, nor do they engage in any ritualistic religious behavior. Rather, the book refers to Christianity only at the theological or philosophical level; and while the struggle between good and evil forces in the world is a central aspect of Christian theology, it is also universal in its scope. Thus while L'Engle makes explicit references to the New Testament, she uses these references merely as a jumping-off point to explore larger, more universal themes.