The aromatic Baeckea frutescens leaves (BFL) known as “Gang-Song-Cha” is a popular drink (Tea) in South China. To explore the healthcare value, a systematic and in-depth study on BFL alleviating rheumatoid arthritis (RA) was carried out by integrating network pharmacology, molecular docking, and experimental verification. The efficacy was first evaluated, and the BFL extract could ameliorate RA by inhibiting articular swelling, lowering immune organ index, improving the ankle pathologies, and regulating serum levels of tumor necrosis factor α (TNF-α), interleukin (IL)-6, and IL-10 in CIA rats. Then the anti-RA mechanism of BFL was investigated by leveraging the high-content and active component 5-hydroxy-7-methoxy-2-isopropylchromone (Chro), and the potential signaling pathway and related target proteins for Chro acting on RA were analyzed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and docking simulation. Finally, the experimental validations were conducted on rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS), and compound Chro could inhibit cell invasion and migration, block cell cycle at G2/M phase and induce apoptosis, and reduce the secretion of inflammatory cytokines by suppressing the PI3K-Akt pathway. These results provided pharmacological basis for the folk usage of “Gang-Song-Cha” for intervening RA.