Polymorphisms of methylenetetrahydrofolate reductase (MTHFR) in hormone metabolism pathways might cause metabolic disturbances and contribute to the development of poly-cystic ovary syndrome (PCOS) and ovarian cancer, but the published studies were in-consistent. The aim of the present study was to evaluate the MTHFR C677T (rs1801133) and A1298C (rs1801131) gene polymorphisms in the risk of PCOS and ovarian cancer by meta-analysis. A comprehensive electronic search was conducted in databases for stud-ies published from 1995 to 2020. The pooled ORs were calculated by Revman 5.2 soft-ware. Twenty-nine articles including 45 case-control studies were included. We found that MTHFR C677T polymorphisms were correlated with elevated PCOS risk (TT vs. CT+CC: OR = 1.41, 95%CI = 1.20-1.67; TT+CT vs. CC: OR = 1.54, 95%CI = 1.07-2.22; CT vs. CC+TT: OR = 1.18, 95%CI 1.04-1.33; TT vs. CC: OR = 1.47, 95%CI = 1.03-2.11; T vs. C: OR = 1.25, 95%CI = 1.06-1.47), which were more obvious in Middle Eastern subgroup. MTHFR A1298C polymorphisms were also associated with overall PCOS susceptibility (CC vs. AC+AA: OR = 2.55, 95% CI = 1.61-4.03; CC+AC vs. AA: OR = 1.84, 95%CI = 1.04-3.28; CC vs. AA: OR = 2.66, 95%CI = 1.68-4.22; C vs. A: OR = 1.67, 95%CI = 1.03-2.71), which were mainly reflected in Asian subjects. For ovarian cancer, MTHFR C677T polymorphisms were only related with elevated ovarian cancer risk in Asian population, while no signifi-cant association was found for A1298C polymorphisms. This meta-analysis suggested that MTHFR C677T and MTHFR A1298C polymorphisms were correlated with elevated PCOS risk. MTHFR C667T only posed a higher risk for ovarian cancer in Asians instead of other populations, while MTHFR A1298C polymorphisms were not related to ovarian cancer risk. Further studies are needed to validate the conclusion.