In this study, phytochemical compositions of Lycium ruthenicum Murray ethanol extract (LRE) were analyzed by LC-ESI-MS/MS and the protective effect of LRE on inflammatory bowel disease (IBD) was evaluated in a dextran sulfate sodium (DSS) induced experimental colitis mice model. The results showed that a total of 129 compounds were tentatively identified, including phenols/phenolic acids, flavonoids and others. LRE supplementation significantly reduced DSS-induced body weight loss, disease activity index increase, colon length shortening and colonic pathological damage. LRE inhibited intestinal inflammation by regulating nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) pathways, restored intestinal immune homeostasis by regulating immune cell infiltration and T lymphocyte subsets, and suppressed (NOD)-like receptor family pyrin domain containing 3 (NLRP3) inflammasome activation. Moreover, the LRE profoundly ameliorated aberrant oxidative stress and restored the intestinal barrier integrity of colitis. Together, LRE supplementation might provide a new dietary strategy for preventing and ameliorating IBD as a functional food.