Yu-Gi-Oh! World Championship 2007 allows users to construct, organize, and duel using the stylus. The game includes 1600 cards, allowing for lots of attacking, spell-casting and defending possibilities. Also, owners of the Yu-Gi-Oh! GX Spirit Caller for DS are able to trade entire decks between the two games and, after beginning the game, can access every card in Yu-Gi-Oh! GX Spirit Caller via the game's card recipe.

Yu-Gi-Oh! World Championship 2007 also includes various dueling possibilities. Different options allow for single-player duels against a host of CPU-controlled opponents; Limited Duels wherein only certain cards are available; and Survival Duels where the aim is simply to beat a succession of duelists for as long as possible. The Trading Card Game is also enhanced via wireless and Wi-Fi modes, allowing players to compete with friends or against players from all over the world.