This study is designed to investigate the protective effect and mechanism of cordycepin on non- alcoholic fatty liver in ob/ob mice. Twelve-week-old male ob/ob mice were divided into 5 groups according to their body weight and blood glucose, and C57BL/6J mice were used in the control group. The animals were orally administered with cordycepin for 7 weeks. Body weight and food intake were measured once a week. Blood were collected from ophthalmic venous and biochemical indexes were determined at the 2nd and 4th week. Insulin tolerance test was performed at the 5th week. After 7 weeks of administration, liver tissues were collected to determine the contents of triglycerides and total cholesterol, and pro-inflammatory cytokines. Liver histology was performed by hematoxylin-eosin and oil-red O staining. Total RNA were extracted from liver tissues and the levels of lipid metabolism-related and inflammation-related genes were detected by real time PCR. Cordycepin effectively reduced the blood lipids level and improved liver function. Nevertheless, it did not improve insulin resistance in ob/ob mice. Cordycepin significantly reduced the contents of triglycerides and cholesterol, and the levels of pro-inflammatory cytokines in liver tissues. Moreover, cordycepin remarkably suppressed the expression of genes related to lipids synthesis and inflammation. These results indicate that cordycepin may improve non-alcoholic fatty liver in ob/ob mice, and the underlying mechanism may be associated with decreased expression of genes related to lipids synthesis and inflammation.