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The role of mycophenolate mofetil (MMF) in the treatment of Graves’ orbitopathy (GO) has attracted much attention. This study is to evaluate the benefit and safety of MMF in moderate-to-severe GO. A meta-analysis of clinical control trials comparing MMF (with or without glucocorticoid (GC)) for the treatment of GO with GC was conducted. We searched the databases, including PubMed, EMBASE, the Cochrane Library, Web of Science, Wanfang, and China National Knowledge Infrastructure (CNKI), for articles published up to 15 June 2022. The primary outcome is referred to the improvement in overall response, and secondary outcomes included the change in clinical activity score (CAS) and adverse events (AEs). Of the 289 articles initially searched, 6 studies were finally eligible for inclusion. The results showed that MMF (with or without GC) was superior to GC in the treatment of GO (OR 3.34, 95% CI 2.17–5.14; p < 0.00001). Subgroup analyses also showed that MMF monotherapy was more effective than GC (OR 4.46, 95% CI 2.52–7.87; p < 0.00001). Compared to methylprednisolone (MP) monotherapy, a combination of MP and MMF was more effective. CAS decreased even more significantly (WMD 0.29, 95% CI 0.10–0.48; p = 0.002) and fewer AEs occurred (OR 0.2, 95% CI 0.06–0.72; p = 0.01) in patients receiving MMF. The pooled data suggested that MMF treatment in GO might be promising. Compared with GC therapy, MMF is safer and more effective. However, more large-sample and high-quality studies targeting MMF use in GO patients and long-term surveillance of prognosis are urgently needed.