The results of epidemiological studies involving omega-3 polyunsaturated fatty acids (PUFAs) and polycystic ovary syndrome (PCOS) are scarce. This matched case-control study assessed the associations between omega-3 PUFAs and PCOS prevalence in 325 pairs of PCOS cases and healthy controls. Dietary information was assessed using a 102-item food frequency questionnaire. Fatty acids in serum phospholipids were measured with a gas chromatography method. We found that omega-3 PUFAs in serum phospholipids were inversely associated with PCOS prevalence, including total, long-chain and individual PUFAs (e.g., docosapentaenoic acid (DPA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)). Compared to the lowest tertile (T1), the adjusted odds ratios (ORs) and their 95% confidence intervals (CIs) for the highest tertile (T3) were 0.63 (0.40, 0.93) for total omega-3 PUFAs, 0.60 (0.38, 0.92) for long-chain omega-3 PUFAs, 0.68 (0.45, 1.01) for DHA, 0.70 (0.45, 1.05) for EPA and 0.72 (0.45, 1.08) for DPA. For dietary intake of omega-3 PUFAs, significant inverse associations were found only for long-chain omega-3 PUFAs (p trend = 0.001), EPA (p trend = 0.047) and DHA (p trend = 0.030). Both dietary and serum omega-3 PUFAs, mainly EPA and DPA, were negatively correlated with PCOS-related parameters, such as BMI, fasting insulin, total testosterone and high-sensitivity C-reactive protein (hs-CRP), but positively correlated with follicle-stimulating hormone (FSH) and sex hormone-binding globulin (SHBG). These results indicated inverse associations between omega-3 PUFAs, especially long-chain omega-3 PUFAs, and PCOS prevalence. Higher intakes of omega-3 PUFAs might be considered a protective factor for PCOS among Chinese females.