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Purpose) To study the component change of urine crystallites with different sizes in the urines of calcium oxalate (CaOx) calculi patients and healthy controls with placement time. (Methods) A combination of high-resolution transmission electron microscopy (HRTEM), fast Fourier transformation (FFT), energy dispersive X-ray spectroscopy (EDS) and X-ray diffraction (XRD) was performed to detect the component of urinary crystallites. Different sizes of urine crystallites were obtained after filtration of urine through microporous membrane with different pore sizes (0.22, 0.45, 1.2, 3, and 8 μm). (Results) The main components of urine crystallites in patients with CaOx calculi are calcium oxalate monohydrate (COM), uric acid, and calcium phosphate. As the placement time increases, the deposition quality of crystallites increased. TEM analysis showed that the amount of small-sized urine crystallites (approximately 100 nm) in the healthy subjects was significantly higher than that of the patients. However, the number of large micron-scale crystals in the controls was reduced remarkably. (Conclusion) The rapid aggregation of urine crystallites may be an important factor affecting the growth of crystallites in CaOx calculi patients. The increase of COM in patient's urine was crucial factors affecting the formation of uroliths.