Objective: To investigate the effective mechanism of Juanbi Granule in treating cold syndrome RA, we performed the transcriptome sequencing and differential expression genes analysis of peripheral blood CD4+ T lymphocytes of patients with Rheumatoid arthritis (RA) before and after being treated with Juanbi granule and healthy people. Methods: A total of 20 patients with rheumatoid arthritis (mean age: (45.8±10.8) years old) were admitted to the Department of Rheumatology and Immunology of the First Affiliated Hospital of Yunnan University of Traditional Chinese Medicine from July 2021 to June 2022 (RA group) were selected, including 13 females (65.0%) and 7 males (35.0%). They were randomly divided into two groups. The control group was treated with oral methotrexate，and the observation group was treated with Juanbi Granule on the control group.At the same time, 10 healthy donors from the physical examination Center of the First Affiliated Hospital of Yunnan University of Traditional Chinese Medicine were selected as the healthy control group (HC group). CD4+ T lymphocytes of Peripheral blood mononuclear cells (PBMC) were isolated by venous blood samples of the two groups of RA patients before and after treatment and of the healthy control group, and transcriptome sequencing was performed. Differential gene expression analysis explored the potential mechanism of Juanbi granule's prescription in treating RA. Results: RNA-seq sequencing results showed that 2053 differentially expressed genes were detected in RA patients compared with healthy controls. These differential gene GO analyses coincide significantly with 12 biological process associated with RA disease in the known GO database. The inflammatory response and the peptidyl-tyrosine phosphorylation were mainly affected in RA patients treated only with methotrexate. However, in RA patients treated with the drug methotrexate and Juanbi granule for one month, enrichment in these related biological process was significantly reduced, and only two related biological process were enriched. After three months of treatment, there was no enrichment in related biological process. Conclusion: Juanbi granule can achieve effective treatment of RA by blocking the biological process highly related to RA disease in CD4+ T lymphocytes.