Rheumatoid arthritis (RA) is one of the most common immune-mediated diseases, and the interaction between the intestinal microbiota and the patient’s immune system may play a role in the occurrence and development of RA. Methotrexate (MTX), as a first-line drug for the treatment of RA, can be directly and indirectly influenced by intestinal microbiota and its enzyme products to affect the bioavailability, clinical efficacy, and toxicity of the drug. Therefore, it is crucial to understand the mechanism by which intestinal microbiota affects RA and the impact of intestinal microbiota on the efficacy of MTX. This article provides a review of the mechanisms by which intestinal microbiota may contribute to the pathogenesis of RA, as well as the role and impact of intestinal microbiota in MTX drug metabolism and treatment response.