Objective: Analysis of the relationship between single nucleotide polymorphisms (SNPs) and outcomes of methotrexate (MTX) therapy for rheumatoid arthritis (RA) in China. Materials and Methods: TYMS 28 bp VNTR (rs34743033), MTHFR [677C > T (rs1801133) and 1298A > C (rs1801131)], ATIC 347C > G (rs2372536), MTR A2756G (rs1805087), and MTRR 66A > G (rs1801394) enzyme proteins may be related to the outcomes of MTX therapy, according to our previous meta-analysis. A total of 162 patients with RA were included in our study. SNPs were evaluated using polymerase chain reaction (PCR). Disease Activity Score 28 (DAS28) was used to evaluate the clinical response, and adverse drug reactions (ADRs) were collected after physical examinations of the patients. Results: The MTHFR 677C > T gene showed a relationship with the ADRs of MTX in the Recessive model [TT vs. (CC C CT)] (p = 0.04, OR = 2.20, 95% CI: 1.01, 4.77). In the Codominant model [CT vs. (CC C TT)], the MTHFR 677C > T gene also showed a trend of association with ADRs (p = 0.08, OR = 0.52, 95% CI: 0.25, 1.08). No significant difference was found between TYMS, MTHFR, ATIC, MTR, and MTRR gene polymorphisms and the RA response or ADRs related to MTX in our study. Conclusion: Our results showed that the MTHFR [677C > T (rs1801133)] TT genotype is associated with ADRs to MTX in Chinese RA patients. Other SNPs, including TYMS 28bp VNTR (rs34743033), MTHFR [677C > T (rs1801133) and 1298A > C (rs1801131)], ATIC 347C > G (rs2372536), MTR A2756G (rs1805087), and MTRR 66A > G (rs1801394) gene polymorphisms, were not associated with MTX treatment outcomes. Further studies are required to validate these findings.