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Background: nsCL/P (nonsyndromic cleft lip with or without cleft palate) is a complex disorder with a multifactorial etiology that involves both genetic and environmental factors. A number of studies identified that MTHFR (methylenetetrahydrofolate reductase) was associated with nsCL/P in different populations. Aim: In this study, we aim to investigate the association between the polymorphism in MTHFR gene (rs1801131, rs1801133) and nsCL/P in Chinese Uyghur population. Subjects and methods: We conducted a case–control study comparing 120 nsCL/P patients to 100 controls. The distribution of MTHFR genotypes and frequency of alleles were compared between patients and controls by chi-square test. The odds ratios (OR) and corresponding 95% confidence intervals (95% CIs) were calculated to estimate the strength of association of MTHFR gene (C677T and A1298C). Results: For rs1801131, allele C frequency was higher in cases than in controls (30.4% > 19.0%), and the difference was statistically significant (χ2 = 7.538, P = 0.006). The genotype distribution at rs1801131 was different between cases (AC > AA > CC, 49.2% > 45.0% > 5.8%) and controls (AA > AC > CC, 65.0% > 32.0% > 3.0%), and the difference was statistically significant (χ2 = 8.883, P = 0.012). AC genotype was found to increase the susceptibility of nsCL/P (OR = 2.219, 95% CI = 1.266–3.892, P = 0.005). No association was found between rs1801133 and nsCL/P. Conclusion: This study indicated that rs1801131 polymorphism in MTHFR was associated with nsCL/P in Chinese Uyghur population. Given the unique genetic and environmental characters of the Uyghur population, these findings may be helpful for exploring the pathogenesis of this complex disease.