The lysosome, an organelle rich in acidic hydrolase, is the main degradation organelle in the cell and is involved in cell processes such as secretion, plasma membrane repair, cell signaling, and energy metabolism. Lysosomal dysfunction may be related to the development of various diseases. In recent years, studies have shown that lysosomal dysfunction may be involved in the development of chronic kidney disease(CKD): lysosomal dysfunction of podocytes interrupts autophagy, inducing transdifferentiation and damage of podocytes. Lysosomal damage mediates apoptosis in proximal tubule epithelial cells via oxidative stress. Lysosomal damage leads to reduced degradation of type I collagen in mesangial cells. Renal endothelial cell dysfunction is closely related to the abnormal expression of lysosomal cathepsin-S and α-galactosidase-A. In summary, lysosomal dysfunction is closely linked to the pathology of intrinsic renal cells. Elucidation of the function of the lysosome in intrinsic renal cells should provide new ideas for clarifying the mechanism of intrinsic renal cell damage in chronic kidney disease.