Dietary supplementation with thymol and carvacrol (CAT) effectively mitigated intestinal inflammation in diarrheic lambs. Multi-omics integrative analyses demonstrated that CAT selectively enriched Romboutsia maritimum, whose metabolic activity led to the production of benzyl cinnamate—a microbial metabolite with potent anti-inflammatory properties. Mechanistically, benzyl cinnamate activated the host glycosyltransferase GALNT7 to upregulate MUC2 expression, thereby promoting mucosal barrier restoration and counteracting E. coli (O157:H7)–induced intestinal injury.