Babesia is a protozoan that mainly parasitizes mammalian red blood cells. It causes damage to multiple organs of the host, even threatening the life of the host when the infection is severe. This study found that the mouse kidney was injured after Babesia infection, leading to changes such as ischaemia and an abnormal morphology of renal and epithelial cells. Serum tests showed that indices reflecting renal abnormalities (including serum creatinine, uric acid, and bilirubin) appeared to be abnormal. To further explore the molecular mechanism underlying kidney injury and self-healing in infected hosts, we employed a data-independent acquisition (DIA) proteomics method to investigate large-scale B. microti infection-induced changes in protein expression and phosphorylation in mouse kidneys. This study identified and analysed the reasons for the obvious changes in kidney injury-related proteins, repair-related proteins, immune-related proteins, and lipid metabolism-related proteins. The results provide a strong theoretical basis for effective treatments of the kidney disease caused by Babesia infection.