Objective To investigate the protective effect of exogenous bone marrow mesenchymal stem cells (MSCs) and CD133+ renal cells in acute renal injury induced by ischemia/reperfusion. Methods A total of 32 male C57BL/6 mice were divided into the normal control group, I/R group, I/R+ MSCs group and I/R+ CD133+ renal cell group, with 8 mice in each group. On the first, second, third and seventh day after the models were established, 2 mice in each group were sacrificed respectively. The blood was sampled to detect the level of blood urea nitrogen (BUN) and creatinine (Cr). The kidneys were prepared for paraffin sections, the pathological changes were observed, and the acute tubular necrosis (ATN) score of kidney tissue was evaluated. The levels of tumor necrosis factor-α (TNF-α) and hepatocyte growth factor (HGF) in kidney homogenate were detected by enzyme-linked immune sorbent assay (ELISA). Results ① The levels of the BUN, Cr, TNF- α and ATN score of the I/R+MSCs group were higher than those of the control group while lower than those of the I/R group, with the most significant difference on the 7th day after operation (P<0.05). The HGF level of the I/R+MSCs group was lower than that of the control group while higher than that of the I/R group, with the most significant difference on the 7th day after operation (P<0.05). ②The levels of the BUN, Cr, TNF-α and ATN score of the I/R+CD133+ renal cell group were higher than those of the control group while lower than those of the I/R group, with the most significant difference on the 3rd day after operation (P<0.01). The HGF level of the I/R+CD133+ renal cell group was lower than that of the control group while higher than that of the I/R group, with the most significant difference on the 3rd day after operation (P<0.01). ③ The levels of the BUN, Cr, TNF-α and ATN score of I/R+CD133+ renal cell group were lower than those of the I/R+MSCs group, while the HGF level was higher (P<0.05). Conclusion Exogenous bone marrow MSCs and CD133+ renal cells may regulate cytokine secretion and improve microenvironment in renal injury by endocrinic approach, which helps the recovery of acute renal injury, and the CD133+ renal cells may be more effective than MSCs.