Objective: To investigate the endocrine and metabolic differences between polycystic ovary syndrome(PCOS) with nonalcoholic fatty liver disease(NAFLD) and without NAFLD. Methods: Body mass index(BMI), waist-to-hip ratio(WHR), blood pressure(BP), uric acid(UA), alanine transaminase(ALT), cortiso1(F), follicle stimulating hormone(FSH), prolactin (PRL), testosterone(T), estradiol(E2), luteinizing hormone(LH), total cholesterol(TC), triglyceride(TG), low density lipoprotein-cholesterol(LDL-C), high density lipoprotein-cholesterol(HDL-C), lipoprotein a[LP(a)], fasting blood glucose(FBG), fasting serum insulin(FINS) and leptin(LEP) levels were measured in PCOS with NAFLD group(PCOS1 group,total number is 27) and PCOS without NAFLD(PCOS2 group,total number is 23). The HOMA-IR was measured too. Results: BMI,WHR,ALT,TG,LP(a),FINS,LEP were lower while HDL-C, F were higher in PCOS2 group than those in PCOS1 group(P < 0.05). HOMA-IR was positively correlated to LEP,BMI,Lp(a) in PCOS1 group, whereas HOMA-IR was positively correlated to T in PCOS2 group. Conclusion: Insulin resistance and dyslipidemia were more frequently observed in PCOS with NAFLD, while PCOS without NAFLD was demonstrated with higher T level. It is definitely that there are a clinical association between PCOS and NAFLD. The intervention and treatment of PCOS should be adopted differently between PCOS with NAFLD and PCOS without NAFLD patients.