The Thousand-Year Door borrows many gameplay elements from its predecessor, the Nintendo 64 game Paper Mario. These elements include a paper-themed universe and a turn-based battle system with an emphasis on action. For the majority of the game the player controls Mario, although Bowser and Princess Peach are playable at certain points. The plot follows Mario's quest as he tries to retrieve the seven Crystal Stars and rescue Peach from the X-Nauts.
The game was well received by critics, attaining an average score of 88 percent from Game Rankings. Critics generally praised the game's engaging plot and gameplay, but criticised it for not being a big progression from its predecessor. The Thousand-Year Door won the "Role Playing Game of the Year" award at the 2005 Interactive Achievement Awards.