Metabolic syndrome (MetS) includes obesity, diabetes, dyslipidemia and hypertension. Its incidence is rapidly increasing worldwide, particularly in postmenopausal women. Estrogens regulate glucose homeostasis and lipid metabolism via estrogen receptors 1 (ESR1) and 2 (ESR2). The current study aimed to elucidate associations of MetS with ESR1 and ESR2 gene polymorphisms in postmenopausal Chinese women. This case-control study included 304 postmenopausal women (154 and 150 control and MetS patients, respectively). Clinical indicators related to MetS were assessed. Two ESR1 (PvuII and XbaI) and two ESR2 (RsaI and AluI) polymorphisms were evaluated by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis. ESR1 polymorphisms were significantly different between MetS patients and healthy controls. G allele frequency for the XbaI polymorphism was significantly higher in patients than in control patients (p = 0.004, OR = 1.610, 95%CI 1.169–2.18). The haplotypes A–T (p = 0.015) and G–C (p = 0.024) showed significant differences. The minor alleles of the XbaI and PvuII gene polymorphisms in both homozygous and heterozygous forms showed associations with elevated waist circumference, fasting serum insulin and HOMA-IR. The minor G allele in homozygous and heterozygous forms of the RsaI and AluI gene polymorphisms showed associations with elevated total cholesterol and LDL-C. In postmenopausal Chinese women, ESR1 polymorphism and the haplotypes A–T and G–C of XbaI–PvuII are associated with MetS, unlike ESR2 polymorphisms. Patients harboring the G allele of XbaI have elevated BMI, waist circumference, systolic and diastolic BP, FBG, HOMA-IR, total cholesterol, TG, LDL-C and NAFLD (%), and reduced HDL-C.