The aim of this study was to investigate the efficacy and safety of Wutou decoction (WTD) in combination with methotrexate (MTX), compared to MTX alone, in early active rheumatoid arthritis (RA) treatment. A total of 92 RA patients were randomly allocated into the WTD&MTX group and MTX only group, at a 1:1 ratio, in this randomized controlled study. Patients in the WTD&MTX group received WTD 10 g/day and MTX 10-15 mg/week for 12 weeks, while patients in the MTX alone group received MTX 10-15 mg/week for 12 weeks. CRP, ESR, DAS28 scores, low disease activity (LDA) rates, remission rates, health assessment questionnaire-disability index (HAQ-DI) scores, and overall response rates were evaluated at baseline (WO), W4, W8, and W12. Adverse events (AEs) were also recorded. Compared to the MTX alone group, the WTD&MTX group disclosed a decreased DAS28 score (P < 0.05) and ESR level (P < 0.05) at W12. The WTD&MTX group also presented an increased percentage of patients achieving LDA at W12 (P < 0.05). In addition, the WTD&MTX group revealed lower HAQ-DI scores than the MIX alone group at W8 (P < 0.05) and W12 (P < 0.01). More importantly, the WTD&MTX group exhibited an elevated percentage of patients achieving overall response, assessed by Clinical Guidelines of New Drugs for Traditional Chinese Medicine (TCM), compared to the MTX alone group at W12 (P < 0.01). No differences in AEs occurrence between the WTD&MTX group and MTX alone group were observed (P > 0.05). In conclusion, WTD in combination with MTX, is more effective and equally tolerated, compared to MTX alone, in treating early active RA patients.