Objective To determine the genotype distribution of methylenetetrahydrofolate reductase (MTHFR) C677T, A1298C and methionine synthase reductase (MTRR) A66G involved in the folic acid biosynthetic pathway among Chinese Han women in Sichuan, so as to provide pregnant women with guidance of supplementing folic acid. Methods By means of Taqman-MGB, 2382 samples from Deyang region in Sichuan province were tested for detecting the genotype distributions and allele frequencies of MTHFR C677T, MTHFR A1298C and MTRR A66G polymorphisms, and then the results were compared with published data in Shandong, Henan and Hainan provinces. Results The allele frequencies of MTHFR C677T were 63.45 and 36.55, those of MTHFR A1298C were 78.20 and 21.80, and those of MTRR A66G were 72.81 and 27.19. There were significant differences in allele distribution of MTHFR C677T and A1298C between Sichuan Han women and other region population. Conclusion This study suggests that the polymorphism of MTHFR C677T and A1298C exhibits region heterogeneity. The polymorphisms of MTHFR may play a role in neural tube defects (NTDs) risk, so periconceptional folic acid supplementation and healthcare following gene polymorphism testing may be a powerful measure to decrease congenital malformations of the central nervous system.