The pathogenesis of urolithiasis is not yet clear， and there are obvious limitations in the prevention and treatment of urolithiasis by either Chinese or western medicine. The microscopic pathological changes of the kidney from anatomical perspective have a certain internal connection with viewpoint of “kidney storing insufficiency， and kidney deficiency as the root” in the traditional Chinese medicine （TCM） zang-fu （脏腑） theory. Accordingly， the prevention and treatment of urolithiasis by integrated traditional Chinese and western medicine based on “shen-kidney” theory has been proposed. It is believed that the prevention and treatment of urolithiasis can be divided into two stages， that is expelling stones and preventing stones. In terms of preventing stones from kideny， it is recommended to focus on the early pathological changes of the kidney； for preventing stones from shen， it is advised to prevent and treat urolithiasis from kidney deficiency. The treatment should be time-based and stage by stage. Adhering to the principle of “prevention before disease occurs， prevention is more important than treatment” aims to advance the intervention targets for the prevention and treatment of urolithiasis. Emphasizing on the simultaneous treatment of kidney disease and urolithiasis， it is critical to put focus on the development of calcium-containing crystalline nephropathy in the early stage of stone formation， as well as the fundamental pathogenesis of kidney deficiency in TCM. Shen-kidney theory aims to further promote the integration of traditional Chinese and western medicine in the prevention and treatment of urolithiasis， which may provide certain reference for solving the current dilemma of urolithiasis prevention and treatment.