Rheumatoid arthritis (RA) is an autoimmune disease that results in a chronic, systemic inflammatory disorder that may affect many tissues and organs, but principally attacks flexible (synovial) joints. Traditional Chinese medicine (TCM) treats RA with herbal formulae according to different syndrome/pattern classification. One important syndrome/pattern in RA is Feng-Han-Shi-Bi. Targeting this syndrome, Juan-Bi-Tang is the basic herbal formula adopted in clinical practises with reliable therapeutic effect. However, the mechanism of Juan-Bi-Tang is still not clear. In this study, we explored the molecular mechanism of Juan-Bi-Tang with in silico analysis on its 11 herbal medicines' chemical compounds, target proteins, protein-protein interaction, and pathway. As a result, the molecular mechanism of Juan-Bi-Tang for Feng-Han-Shi-Bi syndrome in RA covers a variety of biological processes including immune system, signal transduction, metabolism, disease etc. Most of them are relevant to RA which indicate actual therapeutic effect of TCM clinical practises.