Da-Fang-Feng-Tang is a Chinese herbal formula designed to treat syndrome Feng-Han-Shi-Bi for rheumatoid arthritis (RA). Although it's clinical effect have been accepted through 1000 years' clinical practises, its molecule mechanism is still obscure. In this study, by integrating powerful knowledge databases, though bioinformatics analysis, we explored the potential molecular mechanism of Da-Fang-Feng-Tang for RA. The molecule mechanism analysis includes compositional herbal medicine, chemical compound, target protein, RA OMIM genes, and enriched pathways. As a result, Da-Feng-Feng-Tang's 7 target proteins were matched in RA's OMIM genes. What's more, these 7 genes are mainly involved in three pathway hierarchies e.g., disease, immune system, and signal transduction. This research demonstrates that Da-Feng-Feng-Tang's target proteins can regulate a wide range of systems associated with RA. This might indicate that Chinese herbal formula's therapeutic effects are taken effects through system-level regulation rather than targeting only disease specified genes or proteins.