Akkermansia muciniphila (A. muciniphila) plays an important role in intestinal regulation, while it is presently unclear whether live or pasteurized A. muciniphila has different effects on the intestinal health. In the present study, live or pasteurized A. muciniphila was administered to dextran sulfate sodium (DSS)-induced ulcerative colitis mice to investigate its influences on the host intestinal health, gut microbiota, and metabolomic phenotype. The results showed that pasteurized A. muciniphila alleviated the symptoms of colitis in mice more efficiently by encouraging the proliferation of beneficial intestinal bacteria, increasing the production of short-chain fatty acids, and inhibiting intestinal inflammation. Moreover, pasteurized A. muciniphila increased the abundance of Parasutterella and Akkermansia and thus affected the metabolism of lipid and lipid-like molecules associated with lysophosphatidylcholines (LysoPCs). Notably, prophylactic supplementation of pasteurized A. muciniphila increased the relative abundance of the anti-inflammatory microbe Dubosiella, thereby activating intestinal sphingolipid metabolism to alleviate intestinal damage. In conclusion, pasteurized A. muciniphila showed a more effective amelioration of DSS-induced colitis by repairing the dysbiosis of gut microbiota and intestinal metabolism compared to live A. muciniphila, providing a potential strategy to explore the protective effect of A. muciniphila on host intestinal health.