Widely praised for its amusingly absurd characters, whimsical non-logic, and clever wordplay, The Phantom Tollbooth is primarily a story about how to think and learn, with its lessons taught through the extensive use of symbols. Characters, places, and situations stand in for human thought processes, especially two principal aspects of the mind—creativity and logic—and how to blend them effectively to explore the world, acquire knowledge, and use information wisely to contribute to others.

On his journey, protagonist Milo visits two great cities, Dictionopolis and Digitopolis. Dictionopolis grows the letters that help people communicate; Digitopolis mines numbers that help them calculate. In Dictionopolis, Milo learns about the power of words; the city represents the creative, verbal side of the human mind. In Digitopolis, Milo discovers the nearly infinite ways that numbers and reasoning can discover truths about the world; this symbolizes the logical side of human thought.

The cities are at odds because Rhyme and Reason, two princesses who cooperate to create harmony in the land, have been banished. This causes a split between creative thought and logical reasoning among the citizens.