Kidney stones are mainly composed of inorganic crystals such as calcium oxalate (CaOxa). At present, kidney stones can be detected only after their formation, which causes great suffering for patients. If kidney stones can be detected prior to their formation, they can be effectively prevented, which presents great commercial value. In this paper, we review the differences in urine nanocrystallites between stone-forming patients and healthy controls, as well as the relationship between nanocrystallites in urine and the formation of kidney stones. These differences are microcrystalline morphology, aggregation, size and distribution, chemical composition, Zeta potential and stability. The results showed that the formation of kidney stones is closely related to the nature of nanocrystallites. Through the regulation of the physical and chemical properties of nanocrystallites, the formation and recurrence of kidney stones are possibly inhibited.