Previously, our cooperative team confirmed the chemical composition and anti-rheumatoid arthritis (RA) efficacy of Juanbi-Tang (JBT), a clinically and historically used traditional Chinese medicine formula, in two model animals. In this study, we developed an in vivo-in silico strategy to elucidate the anti-RA material basis and mechanism of JBT. With the aid of high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC-Q-TOF), the metabolic profiles were investigated in normal and collagen-induced arthritis RA rats following oral administration of JBT. Based on the absorbed constituents in RA rats, network pharmacology was employed to predict the anti-RA mechanisms, followed by molecular docking validation. Consequently, there were 18 absorbed compounds with 6 chemical structures, which were absolutely identified by matching with standard compounds in plasma, and 17 generated metabolites involved of 7 biotransformation pathways, including glucuronidation, sulfation, hydroxylation, deglycosylation, methylation, taurine, and glycine conjugation. Moreover, RA disease affected the absorption and metabolism of the constituents in JBT, given the undetected 2 absorbed compounds and 4 metabolites in RA rats. The analysis of network pharmacology indicated that those absorbed compounds in JBT may fight against RA through the MAPK, FoxO, and Rap1 pathways. Molecular docking also validated these results. Overall, this is the first study to describe the metabolic profiles of JBT-treated healthy and RA rats, and it provides a possible anti-RA mechanism through multiple absorbed compounds and targets by network pharmacology.