The difference of urine crystallites under 1000 nm in 10 patients with urolithiasis and 10 healthy subjects with no history of urolithiasis was comparatively studied with the nanoparticle size analyzer. By comparing the differences of intensity-autocorrelation curve, polydispersity index (PDI), Zeta potential, and relative error of average diameter of the two kinds of urine crystallites, it was concluded that the urine crystallites of healthy subjects were more stable than those of patients. The urine crystallites of healthy subjects had a narrower size distribution from 100 nm to 350 nm and a better dispersion (PDI < 0.3). However, the urine crystallites of patients with urolithiasis had a wider distribution from dozens of nanometers to 1000 nm and a worse dispersion (PDI > 0.5). The best processing method for urine crystallites detection was found: after antisepticising and protein-coagulating with formaldehyde, the urine was diluted with distilled water of the same volume, then filtrated through a micropore film of 3 microm, and the filtrate was centrifugalized at 4000 rpm for 15 minutes. This method can remove the cell fragments and macromolecular substances in the urine without affecting the detection of the urine crystallites under 1000 nm. The results were consistent with those obtained by transmission electron microscope (TEM).