In clinical fights against rheumatoid arthritis (RA), tofacitinib and glucocorticoids are usually combined with Chinese medicines in China for better therapeutic effects against inflammation (9.6 days of average hospital stay, 73% reduced C-reactive protein, 69% decreased erythrocyte sedimentation rate) with fewer side effects of osteoporosis (16.6% RA patients were diagnosed with osteoporosis compared with around 30% onset ratio without Chinese medicines). To discover the candidate mechanisms of Chinese medicines against RA and osteoporosis, bioinformatics analysis was launched with hospitalized data, blood tests, and microarray. As a result, six top Chinese medicines were identified to deliver significant coordinative regulation networks against RA inflammation while reducing osteoporosis with their bioactive compounds, targeted genes/proteins, and genes/proteins associated with RA and osteoporosis.