By means of X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), nano-particle size analyzer, scanning electron microscopy (SEM) and transmission electron microscopy (TEM), the composition, morphology, particle size and zeta potential of urinary microcrystalline in urine of magnesium ammonium phosphate stone formers were investigated. The components of stones were also analyzed. The results showed that there was a close relationship among stone components, urinary microcrystalline composition and urine pH. A high pH value of 6.5 or more usually appeared in the urine of magnesium ammonium phosphate stone formers. The main component of urine microcrystalline was magnesium ammonium phosphate crystals with different crystal water such as monohydrate or hexahydrate. Magnesium ammonium phosphate crystals are mainly petal-shaped, crosswise shape. These microcrystalline have an uneven particle size distribution, a wider distribution range, and apparent aggregation. There is no significant difference in the zeta potential between the magnesium ammonium phosphate stone formers (mean (-9.83±0.66) mV) and healthy control subjects (mean (-10.74±0.25) mV). This study can help predict the occurrence of urolithiasis, and provide inspiration to the prediction of the type of urinary stones.