[Purpose] This study aimed to study the kinetic aggregation of urine crystallites with different sizes in the urines of calcium oxalate (CaOx) calculi patients and healthy controls. [Methods] We studied the property changes in crystallites with different sizes by nanoparticle size analysis and transmission electron microscopy (TEM) in two types of urine filtered through a microporous membrane of 0.22, 0.45, 1.2, 3.0, and 8 μm. [Results] The measured Zeta potential in the two types of urine crystallites and polydispersity index showed that the urine crystallites of the patients were rapidly aggregated, whereas those of the controls were only slightly or slowly aggregated with increased placement time from 1 h to 8 h. The small-sized urine crystallites were easy to aggregate than the large-sized ones. [Conclusion] The urinary system of calculi patients is unstable and very susceptible to urine crystallite aggregation. The rapid aggregation of urine crystallites may be an important factor affecting the growth of crystallites in CaOx calculi patients.