This study aimed to examine the regulatory effects of moxibustion on macrophage polarization and migration in a rat model of rheumatoid arthritis, as well as the role of T cell immunoglobulin and mucin domain–containing protein 3 (TIM-3) in this process. On day 0 of the experiment, Sprague–Dawley (SD) rats were divided into five groups. Complete Freund’s adjuvant (CFA) was injected into the hind footpads to establish the rheumatoid arthritis model. Additionally, lentivirus-mediated Havcr2 RNA interference (LV-Havcr2-RNAi) was injected into the hind footpads to inhibit TIM-3 expression. Starting on day 7, rats underwent moxibustion treatment in cycles comprising six days of treatment and one day of rest, for a total of three complete cycles. After completion of moxibustion therapy, the inflammatory status was assessed through histological analysis and measurement of paw thickness. Phenotypic markers of M1 and M2 macrophages were assessed by enzyme-linked immunosorbent assay (ELISA) and immunofluorescence. TIM-3 expression was detected via quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot. Furthermore, peritoneal exudate macrophages (PEMs) were isolated from additional SD rats, and macrophage migration was examined using a Transwell assay. The study found that after CFA injection, rats exhibited significant paw redness and swelling, along with an imbalance in macrophage phenotype expression. Additionally, Transwell migration assays revealed that CFA-induced model rats showed increased macrophage migration relative to control specimens. However, moxibustion treatment attenuated these changes. Results also demonstrated that moxibustion increased TIM-3 expression, and after lentiviral intervention, TIM-3 levels were markedly reduced, leading to exacerbation of inflammatory manifestations and macrophage imbalance. These results indicate that TIM-3 serves as a key mediator in moxibustion regulation of macrophage polarization and migration.