Aim To explore the effect and mechanisms of matrix metalloproteinase-9 （MMP-9）/tissue inhibitor of metalloproteinase-1 （TIMP-1） in ApoE^－/－ mice kidney damage induced by hyperhomocysteinemia （HHcy）, provide theoretical and experimental basis for the prevention and treatment of kidney disease, and supply a new indicator for kidney disease surveillance. Methods 5 week old male ApoE^－/－ mice were divided into three groups: ApoE^－/－ control group, ApoE^－/－ high methionine diet group and ApoE^－/－ intervention group, and 5 week old SPF male C57BL/6J mice were chosen as normal control group. After fed for 14 weeks, the serum concentration of homocysteine （Hcy）, creatinine （Cr） and urea were detected by biochemical analyzer, transmission electron microscopy and PAS staining were used to show the damage of kidney. MMP-9 and TIMP-1 mRNA expression levels of kidney were detected by real-time PCR, MMP-9 protein expression of kidney was assayed by immunohistochemical staining and TIMP-1 protein expression was detected by ELISA. Results Compared with normal control group, the serum concentration of Hcy, Cr and urea of ApoE^－/－ high methionine diet group were significantly increased by 3.66-, 1.1-and 1.6-folds （P<0.01）. Transmission electron microscopy and PAS staining showed that kidney damage of ApoE^－/－ high methionine diet group were more serious than normal control group. Real-time PCR results showed that mRNA expressions of MMP-9 and TIMP-1 were evidently increased by 5.25-and 1.38-folds respectively （P<0.01）. The results of immunohistochemistry assay showed that protein expression of MMP-9 in ApoE^－/－ high methionine diet group was significantly higher than that in the normal control group （P<0.01）, ELISA assay showed TIMP-1 protein expression in the ApoE^－/－ high methionine diet group was significantly higher than that in the normal control group （P<0.01）. Compared with ApoE^－/－ high methionine diet group, Hcy levels decreased in ApoE^－/－intervention group （P<0.01）, and Cr and urea levels were significantly decreased （P<0.01）. Transmission electron microscopy and PAS staining showed that kidney damage of ApoE^－/－ intervention group were relieved compared with high methionine diet group. Serum Hcy level was positively correlated with Cr and urea （r²＝0.4344, P<0.0001 r²＝0.4478, P<0.0001）, and also with the ratio of MMP-9/TIMP-1（r²＝0.39309, P<0.001）. And the ratio of MMP-9/TIMP-1 was positively correlated with Cr and urea （r²＝0.1464, P<0.05 r²＝0.3027, P<0.01）. Conclusions HHcy could cause the up-regulation of MMP-9/TIMP-1 and degradation of extracellular matrix, then lead to ApoE^－/－ mice kidney damage.