Kidney stones are a common and frequently-occurring disease of the urinary system worldwide, and their recurrence rate is still high. It is generally believed that the supersaturation of salts in urine and the lack of substances to inhibit the formation of crystals in the urine are the main causes of kidney stones. The etiology of kidney stones is complex. At present, a variety of theories about the etiology of kidney stones have been put forward, mainly from the aspects of heredity, disease, metabolism and eating habits, to study the etiology of kidney stones to infer the causes of different kinds of stones, and then make targeted treatment plans. However, the clinical effect of internal medicine treatment of kidney stones is still limited. Actively exploring the growth mechanism of stones will undoubtedly be of positive significance to the scientific treatment of kidney stones. It is important to observe the internal structure of the stones and infer the formation and growth track of the stones according to these structural characteristics. It is difficult to obtain the internal structure of kidney stones by traditional research methods, so there are few reports on the microstructure of kidney stones. The appearance of high-resolution microCT, especially synchrotron X-ray microCT, can undoubtedly provide advanced detection means for this research. As the third generation of high-quality synchrotron radiation source, Shanghai synchrotron radiation facility (SSRF) has the advantages of high photon flux, collimation, polarization, coherence and wide spectrum. The synchrotron radiation X-ray detector can realize the fast and non-destructive detection of accurate and sensitive tissue structure information. It can reproduce the three-dimensional microstructure inside the sample on the premise of maintaining the integrity of the sample. Thus, this new detection method overcomes the limitations of traditional two-dimensional slicing technology, such as destroying the integrity of tissue structure and being, unable to accurately obtain the three-dimensional spatial information as well as matrix composition of tissue structure. In this study, the X-ray microCT technique at SSRF was used to analyze the microstructure of kidney stones from 32 patients. The research results showed that there were obvious differences in the internal structure of kidney stones, which could be divided into six types: Ⅰ the two-phase compact type; Ⅱ the crystalline type; Ⅲ the continuous multilayer deposition type; Ⅳ the discontinuous multilayer deposition type; Ⅴ the mosaic porous type; Ⅵ the composite type. The results of this study would contribute to reveal the growth mechanism of kidney stones further, and provide a new scientific perspective and basis for more accurate treatment of kidney stones.