L-Carnitine is widely recognized for its involvement in lipid metabolism, but its effects on muscle quality and gut health in carp have not been well studied. The research aimed to investigate how L-carnitine influences muscle quality and intestinal health in high-fat-fed carp. The study was separated into four groups that received either the standard diet, a high-fat diet (HFD), or a HFD supplemented with 500 mg/kg L-carnitine (LLC), or a HFD supplemented with 1000 mg/kg L-carnitine (HLC) for 56 days. L-Carnitine was found to significantly reduce blood lipid levels. In addition, L-carnitine increased the crude protein content and decreased the crude fat content of high-fat-fed carp muscle while improving muscle fiber morphology and muscle quality. L-Carnitine increased the expression of genes related to intestinal tight junction proteins (claudin-2, occludin, and zo-1), improved the expression of genes related to intestinal inflammation, and enhanced the physical barrier function and organization of the intestine. Analysis of intestinal flora and intestinal metabolites showed that L-carnitine increased the diversity of the intestinal flora, increased the abundance of Cetobacterium, and influenced intestinal levels of bile acids, arachidonic acid, and tryptophan-related metabolites. In conclusion, supplementation with 1000 mg/kg L-carnitine improved muscle quality and intestinal health significantly in high-fat-fed carp by regulating muscle nutrient metabolism and intestinal flora.