To study the formation mechanism of magnesium ammonium phosphate (MAP) stones. X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), and nanoparticle size analyzer were used to investigate the nanocrystallites in urines of 10 MAP stone patients and 10 healthy persons. Most of the nanocrystallites in healthy urines were uric acid, calcium oxalate dihydrate (COD), β-Ca3(PO4)2 and NH4MgPO4. However, there were mainly MAP·6H2O, calcium oxalate monohydrate (COM), hydroxylapatite, β-Ca3(PO4)2 in the urine of MAP stone patients. The sizes of nanocrystallites were ranged from 22-68 nm in healthy urines and 17-92 nm in lithogenic samples. The stability of nanocrystalline in healthy urines was better than that in lithogenic samples. The nanocrystallites in MAP stone patients have a large size variation and a poor stability, easily aggregated to each other and contained more COM crystals which having a strong adhesion ability to cell membrane. All these factors promote the formation of kidney stones.