The relationship between n-3 PUFA and metabolic syndrome (MS) is not clear. The aim of this study was to examine relationships between plasma phospholipids (PL) n-3 PUFA and MS in Chinese subjects. Nine hundred and twenty-nine subjects were recruited in Hangzhou, China. Two hundred and ten (183 males, 27 females) with MS and 719 (545 males, 174 females) healthy subjects were identified in this cross-sectional study. The prevalence of MS in females (24.56%) was significantly higher than that in males (10.04%) in this population. Total PUFA (p<0.001), n-3 PUFA (p<0.001), and n-3:n-6 (p<0.001) were significantly lower in MS subjects compared to healthy subjects. Plasma phospholipid (PL), n-3 PUFA was significantly inversely associated with MS (p = 0.013). In addition, subjects with high levels of PL total fatty acids (FA) had a more than threefold higher likelihood of MS (OR = 3.44, 95% CI = 1.60-7.39) than the subjects with low levels of PL total FA. Our results suggest that plasma PL n-3 PUFA was significantly inversely associated with MS, while high total FA were positively associated with MS in Chinese.