The Crystal Pearl is a key object required in order to pass the Magic Exam.
In the Magic Exam, only one two-man team is allowed to pass. For a pair to pass, they must have the Crystal Pearl in their possession by the time the Exam comes to an end. The Crystal Pearl is presumably only used for one Magic Exam, the one in the first series.The Crystal Pearl is dropped into the human the world and the rest is up to the examinees. Each team gets a tracking device that is capable of sensing the Crystal Pearl. The Crystal Pearl ends up falling onto the plate of one unexpecting human, Nina Yamada, who mistakes it for a candy that came with the cake she ordered. Her friends suggest that she eat it, and she puts it in her mouth and tries to chew it with little success, When the two wizards Zero and Ichî surprise her with their arrival, she ends up swallowing the Pearl whole. Upon finding this out, Zero and Ichî call the exam headquarters, who say that they should be able to make a potion that will remove the Pearl from Nina's body intact in several months. Seeing no other option, the two plan on protecting Nina and the Pearl inside her until they can get the potion so that they can ace the exam.
Some examinees, however, are not so patient. Realizing that Nina has accidentally swallowed the Pearl, they note that there is nothing in the rules that forbids killing humans, and so they plan on killing her in order to take the Pearl from her body. The only other pair that seems to want to spare Nina is Nanase and Yakamo (or rather, Yakamo, as Nanase would prefer to just kill Nina and be done with it).
In the anime, when Nina takes the potion so that Zero and Ichî won't have to keep getting hurt in order to protect her, the Pearl comes out of her body and grows into a giant and tainted Black Pearl. With the help of several examinees and the assistance of Rill, the Pearl is defeated and returns to it's original size. The Pearl hatches into a small dragon that is apparently Nina's familiar, having grown a bond with her after spending so much time in her body. In the manga, there is not Black Pearl, but the Pearl still ends up hatching into a dragon which, in the manga, Nina names Pearl, after the Crystal Pearl itself.