Maca is a functional food with anti-inflammatory activity, and it is rich in protein. Currently, inflammatory bowel disease (IBD) is a common gastrointestinal disease. However, there is little research focusing on the effect of maca protein (MCP) on IBD. In this study, we extracted MCP from maca root and explored its effect and mechanism on improving dextran sodium sulfate (DSS)-induced IBD in mice. The results indicated that MCP intervention alleviated the clinical symptoms and colon tissue damage of mice with DSS-induced colitis and inhibited the expression of inflammatory factors. Moreover, it can modulate the gut microbiota composition in mice with DSS-induced colitis. The regulation is achieved by reducing the relative abundance of the IBD-exacerbating key bacterial genera: Lachnospiraceae_NK4A136_group, Bacteroides, Desulfovibrio, Prevotella, Helicobacter and Sutterella, while increasing the relative abundance of the IBD-alleviating key bacterial genera: norank_f_Muribaculaceae, Lactobacillus, Oscillospira, Akkermansia and Bifidobacterium. MCP can also promote the production of short-chain fatty acids (SCFAs). The further western blotting results indicated that MCP can regulate the Treg/Th17 immune balance in mice with colitis via the SCFAs-GPR41/43/HDAC1 signaling pathway. Overall, MCP can alleviate colitis by comprehensively regulating the gut microbiota and inflammatory response. It may be a promising functional component that reduces the risk of colitis by maintaining intestinal health.