Cassane diterpenoids (CAs), recognized as main constituents of many medical plants of the genus Caesalpinia, exhibit diverse bioactivities, including anti-inflammatory and immunomodulatory activity, and also showed a therapeutic effect on rheumatoid arthritis (RA) according to previous work, including ours. In this study, 102 CA compounds were selected to explore the possible molecular mechanism of this class of natural products on anti-inflammatory and immunomodulatory activity using RA as a disease model through a series of in silico methods: chemical-similarity-based target prediction, molecular docking, and molecular dynamics (MD) simulation. As a consequence, four signaling pathways (TCR signaling pathway, TLR signaling pathway, VEGF signaling pathway, and osteoclast differentiation pathway) by which CAs exert their effect on inflammation and immunomodulation were identified. Furthermore, the binding modes of CAs complexing with several crucial targets, which were picked out by credible docking results and took part in these signaling pathways, were explored by MD simulations. This is the first time that the molecular mechanism of the anti-RA activity of natural CAs has been investigated with in silico methods, and these findings might explain the activity of CAs on anti-inflammation and immunomodulation, which could supply a valuable reference for drug design research on CAs.