Black rice and black bean have not yet been fully investigated as healthy foods for their therapeutic effects on type 2 diabetes mellitus (T2DM). In this study, we aimed to evaluate the antidiabetic effects of black rice, black bean husk anthocyanin extracts, and their combination on glycolipid metabolism, gut microbiota, and serum metabolites in T2DM rats. Black bean husk and black rice anthocyanin extracts were administered to T2DM rats by gavage for 4 weeks. The results showed that black rice and black bean husk anthocyanin extracts significantly improved blood glucose, insulin resistance, serum oxidative stress state, lipid metabolism and inflammatory cytokines levels in rats, and alleviated liver damage. Black rice and black bean husk anthocyanin extracts increased the abundance of short-chain fatty acid (SCFA) producing bacteria Akkermansia spp., Phascolarctobacterium spp., Bacteroides spp., and Coprococcus spp., changed the gut microbiota structure; activated AMPK, PI3K, and AKT; inhibited HMGCR, G6pase and PEPCK expression; and inhibited hepatic gluconeogenesis. Moreover, by adjusting the levels of urea, deoxycytidine, L-citrulline, pseudouridine, and other serum metabolites in T2DM rats, the arginine biosynthesis and pyrimidine metabolism pathways were downregulated. The above results indicated that black rice and black bean husk anthocyanin extracts had a significant impact on the development of T2DM.