Type 2 diabetes mellitus (T2DM) is a prevalent metabolic disease, yet its pathogenesis remains inconclusive. Recent studies have revealed a close relationship between the gut microbiota and T2DM, and specific gut microbiota structures and metabolic characteristics are associated with the onset and progression of T2DM. Exercise is an effective intervention for the prevention and management of T2DM, capable of reversing the dysbiosis induced by T2DM and regulating gut metabolites. However, the effects of exercise on the gut microbiota in T2DM patients still present many unresolved issues. Furthermore, the regulation of gut microbiota by exercise in T2DM patients is closely linked to multiple organs and can exert alleviation effects on T2DM via various gut-organ axis pathways. This paper reviews the characteristics of gut microbiota in T2DM and the effects of exercise on the gut microbiota in T2DM, with a particular focus on the mechanisms by which exercise regulates the gut microbiota to ameliorate T2DM via the gut-organ axis. This review aims to provide a reference for elucidating the relationship between exercise, gut microbiota, and T2DM.