Fang-Feng-Tang is a Chinese herbal formula which is designed to treat syndrome Feng-Han-Shi-Bi for rheumatoid arthritis (RA). Although its therapeutic effects are widely accepted, its mechanism is still obscure. In this study, by integrating leading knowledge databases of associated different domains, we explored Fang-Feng-Tang's potential therapeutic agents for RA through targeted pathway hierarchies. The molecule mechanism analysis includes compositional herbal medicine, chemical compound, target protein, and pathways enriched. Target proteins are restricted with RA OMIM genes and FDA approved RA drug targets for partial validation. As a result, 8 target proteins were matched and they are UGT1A9, GNT1, UGT1, JAK3, CCR2/5, and CMKBR2/5. What's more, they are mainly involved in pathways of signal transduction, metabolism, immune system, and disease. This research demonstrates that Feng-Feng-Tang's target proteins may regulate a wide range of different systems. This might indicate that Chinese herbal formula's therapeutic effects can be demonstrated through system-level regulation rather than targeting disease specified genes or proteins.