Background: Rheumatoid arthritis (RA)-interstitial lung disease (RA-ILD) is an idiopathic complication of RA that presents as pulmonary fibrosis. Despite extensive research, the exact cause of RA-ILD remains elusive, driving the ongoing search for effective treatments. Methods: Transcriptomes of lung tissues from both healthy individuals and patients with RA-ILD were analyzed to identify differentially expressed genes. CMAP identified the flavonoid naringin (NAR) as a potential drug for RA-ILD treatment. Subsequently, NAR nanoparticles were developed and orally administered to a collagen-induced arthritis ILD (CIA-ILD) model in DBA/1 mice. Transcriptome and protein profiling analyses using microscale thermophoresis and cellular thermal shift analysis were conducted to predict and confirm the downstream molecules and targets of NAR therapy in RA-ILD. Additionally, an in vitro pulmonary fibrosis model was established to investigate the specific mechanism of NAR treatment in CIA-ILD. Results: In animal experiments, treatment with NAR nanoparticles significantly reduced pulmonary fibrosis in CIA-ILD mice compared with untreated mice. Moreover, there was a notable increase in the number of lymphatic vessel endothelial receptor-1 positive (LYVE1+) macrophages in the lung tissue. Mechanistically, NAR increased LYVE1 levels in macrophages by targeting 14-3-3 zeta. In vitro experiments demonstrated that NAR-treated LYVE1+ bronchoalveolar macrophages (LYVE1+ BLM) effectively inhibited epithelial-mesenchymal transition of A549 cells and fibroblast-myofibroblast transition of HFL1 cells by reducing the secretion of transforming growth factor beta-1. Conclusion: Our research revealed NAR as a novel reference drug for treating RA-ILD, while also identifying potential therapeutic target cells and avenues for drug development in this context. Further comprehensive research is warranted to extend these findings and benefit a broader population of patients with RA-ILD pulmonary fibrosis.