The gameplay of Crystal Monsters involves the capture and training of a variety of creatures called monsters. Monsters can learn up to four moves called skills. Just like in most RPGs, monsters are able to gain experience points and level up after battles, making them stronger.

Essence Cores of each monster type are used to capture specific wild monsters, though they may break free at times.  The less HP the monster has, the greater the percentage chances.  The higher the level of a monster, the  easier it will be to capture (e.g. a LV30 Tadpolaris will make catching a LV22 Tweetmare Plus much easier). If it’s captured, it will be put in storage.

You can't capture a trainer's monster, boss or mid-boss. Evolution Stones can be used to evolve most monsters.  Upon evolving, monsters learn additional skills and gain higher stats.  There are two stages of evolution: Plus and Mega.  They can occur after a monster reaches a certain level.

Crystal Monsters uses a turn-based system.  When you encounter a wild monster or challenge a trainer, the screen changes to a battle scene with the opposing monsters and an option menu.  You may have up to three monsters on your team.  You can attack, pass to the next monster on the team, use an item or flee the fight.

Most of the battles you'll face will be random battles with wild monsters, as there is a low number of trainers, bosses and mid-bosses in this game.  Wild monsters can be found in routes, dungeons, sidequests, etc.  The encounter rate is inconsistent, though, as monsters may appear often or pop up only rarely.

If a team member faints, it will be removed from the team and put in storage.  In battles with trainers, mid-bosses or bosses, you'll lose and get a Game Over if you have no usable monsters left on your team.  However, in fights with random wild monsters, if you have other monsters left in storage, the strongest one will be added to your team and you won't get a Game Over.