Crystal Castles has nine levels with four castles each, and a tenth level which features a single castle — the clearing of which ends the game.
Each of the 37 trimetric-projected castles consists of a maze of hallways filled with gems and bonus objects and also includes stairs, elevators and tunnels that the player can use as shortcuts. The three-letter initials of the player with the highest score are used to form the first level's castle structure. When all gems in a castle have been collected, a tune of the Nutcracker Suite is played, and the player moves on to the next castle. The player can also skip some castles and acquire additional lives and points by using secret warps activated by making Bentley Bear jump at special locations.
A trackball and jump button are used for controlling Bentley Bear's motions. Gems are collected by walking over them, and a bonus is given upon collection of the last gem. While collecting gems, there are a number of enemies that try to stop Bentley and/or collect the gems for themselves. Any gems collected by the enemies also result in a lower obtainable score for that screen. Likewise, if the last available gem is collected by the enemy, the player also loses the last gem bonus.
Enemies can be avoided by use of the maze and its constructs, or by making Bentley jump over opponents with the jump button, in some cases also allowing him to stun them. Some types of enemies will track Bentley's movements in certain ways, while others move at random. If Bentley is touched and loses a life, he "cries out" in a distinctive manner with the use of a cartoonish speech balloon. If at least 3 lives remain, he says "BYE!"; if 2 lives still remain, the quotation is "OH NO!"; if 1 life is left, it is "OUCH!"; and finally, for the last lost life (which ends the game), he says "#?!", so as to imitate an obscenity.