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 cold syndrome Rheumatoid arthritis(RA) before and after being treated with Juanbi Granule and healthy people. Methods Between July 2021 and June 2022, a total of 20 rheumatoid arthritis patients (RA group) were selected from the inpatient rheumatology department of the First Affiliated Hospital of Yunnan University of Chinese medicine as the study subjects, of which 13 (65.0%) were female and 7 (35.0%) were male, with a mean age of (45.7 ± 10.8) years old. They were allocated into two groups randomly. The comparison group was treated with methotrexate by mouth, and the intervention group received Juanbi granules on the basis of the comparison group‘s treatment. At the same time, 10 healthy donors from the physical examination Center of the First Affiliated Hospital of Yunnan University of 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 2 053 differentially expressed genes were detected in RA patients compared with healthy controls. These differential gene GO analysis 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.