Rheumatoid arthritis (RA) constitutes a chronic, progressive autoimmune disease, and effective treatment of RA remains a challenge. Due to the multiple side effects and "therapeutic ceiling" effect of current RA medications, it is essential to find natural alternatives and explore their mechanisms of action in RA. In this study, we analyzed the targets of action and signaling pathways of gentiopicroside (GEN) in RA using network pharmacology and validated them through molecular docking and experimental approaches. A collagen-induced arthritis (CIA) rat model was employed to analyze the role of GEN in influencing RA joint pathology and related angiogenic factors. Additionally, cellular experiments were conducted to assess the proliferation, migration, and tubular structure formation ability of endothelial progenitor cells (EPCs). Western blotting was used to detect the protein expression of CXCL12 and CXCR4. Network pharmacological analyses revealed that GEN exerts multiple effects on RA therapy by modulating multiple pathways. Combined with literature analysis and molecular docking data modeling, GEN was found to intervene in RA by regulating CXCL12 and CXCR4. In CIA rats, GEN inhibited the expression of HIF-1α, CXCL12, VEGF-A, and Ang-2, and attenuated the pathology associated with aberrant neovascularization in the knee joint. Cellular experiments confirmed that GEN could inhibit the proliferation, migration, and tubular structure formation ability of EPCs induced by high-mobility group box 1 (HMGB1), and could inhibit the formation of abnormal neovascularization by interfering with CXCL12 and CXCR4. GEN demonstrates a significant effect in inhibiting abnormal neovascularization and can regulate CXCL12 and CXCR4 to intervene in the pathological progression of RA. This study provides a novel approach for the treatment of RA and a theoretical foundation for further research.