Metabolic syndrome (MetS) has become an important issue in the healthcare systems of both developed and developing countries. Phytoestrogens have shown estrogenic effects, which may involve in the etiology of MetS. The current study consisted of 293 MetS cases and 264 healthy controls. The concentrations of seven plasma phytoestrogens (daidzein, genistein, glycitein, equol, enterolactone, enterodiol and coumestrol) were detected by UPLC-MS/MS. Adjusted unconditional logistic regression was used to assess the associations between plasma phytoestrogens concentration and risks of MetS, as well as the associations between plasma phytoestrogens concentration and MetS components. Linear regression was used to evaluate the associations between equol concentration in equol-producers and MetS components. Higher concentrations of total isoflavone and equol were associated with decreased risk of MetS. The equol concentration was negatively associated with waist circumference and positively associated with HDL-C level. Increased daidzein was associated with both lower waist circumference and lower fasting blood glucose levels. Our results suggested that higher plasma total isoflavone, equol and daidzein might decrease MetS risk.