Final Fantasy Crystal Chronicles is an action role-playing game where players take control of a group of adventurers who travel the world searching for rare trees which produce "myrrh", used to fuel crystals protecting the world's settlements from the poisonous Miasma.[4][5] Players are guided through a repeating series of events which dictate their progress through the game and its story. The adventurers set out from their village, travelling to the trees guarding the vessel which gathers the myrrh, exploring dungeons in which the trees reside, then returning home to renew their village's protective crystal.[6]: 12–13 
Players choose their avatar character from one of four races; they can be male or female, each with four pre-set body types. Each race has specific strengths, such as the human-like Clavats having high defence and magic statistics and the nomadic Selkies being able to use special abilities with less cooldown time. Each character's attributes are further customised by choosing the profession of their family, which gives the character access to unique facilities and items each time they return to their home town.[4][5] Players navigate the world map with their Caravan, and enter town and dungeon environments discovered during the journey. In towns, the player can freely explore and use the available facilities to create and upgrade both items and equipment using materials and blueprints gathered during their journey. The player can also encounter other caravans and travellers, triggering story events.[4][6]: 28–33  Items used to support the player are both bought in shops and received as gifts from the player character's family.[6]: 28–33 
While exploring dungeons, players are confined to a safe zone created by the vessel, fighting enemies in a style similar to hack and slash games with actions assigned to command buttons; actions can be chained together into short combination attacks using equipped weapons to increase damage and charge up magic abilities. Magic can be used to damage enemies or trigger status ailments, with multiple spells able to fuse and create new effects in battle.[4][7] The elemental affinity of the player's attacks can be changed using crystals found in dungeons. Certain elemental affinities are necessary for crossing into new zones otherwise blocked by streams of Miasma.[6]: 28–33  Instead of an experience point system, character attributes and statistics are increased by completing challenges in each dungeon session which award skill points, and Artifacts found in dungeons which can be equipped to a character.[6]: 28–33 [7]
In single-player, the player controls one character guarding the Moogle-held vessel from monster attacks while navigating dungeons.[6]: 14–20  The game's multiplayer allows up to four players to join in a local gameplay session; multiplayer relies on the GameCube console linking with the Game Boy Advance (GBA) link cable. All players are displayed on the screen, while their GBAs both control their characters and allow functions such as shopping in towns and performing battle functions.[6]: 21–26 [7] Character attributes are increased in the same way, except that the necessary points are given to the best player during that session.[7] In battle, players can raise attack meters using standard attacks in succession, and combine individual spells to create more powerful versions for higher damage.[5] The link cable can also be used in single player, allowing the GBA to be used both as a controller and a second screen displaying radar information. The type of radar and what it shows is determined by the color the player's Moogle—one of a recurring Final Fantasy race—is painted during stays in towns and visits to the adventurers' hometown.[6]: 14–20 [8]