This study investigated the effects of a fulvic acid–based functional feed material (FBFM)—a mixture of fulvic acid and a Clostridium butyricum fermented suspension—on the growth performance and physiological adaptation of large yellow croaker (Larimichthys crocea) exposed to summer heat stress, using a multi-omics strategy. Fish were fed diets containing different concentrations of FBFM for 60 days and assessed for growth performance, antioxidant status, hepatic gene expression, liver and intestinal metabolism, and gut microbiota composition. Results showed that the group receiving 1.5 g/kg FBFM (FBFM3) exhibited the highest average weight gain, survival rate, and specific growth rate, along with significantly enhanced activities of antioxidant enzymes (CAT, SOD, GSH-Px, T-AOC) in both the liver and the intestine. Transcriptomic profiling of the FBFM3 group revealed significant upregulation of genes involved in the TCA cycle and oxidative phosphorylation pathways, while metabolomic analysis indicated increased levels of short-chain fatty acids and metabolites associated with bile acid biosynthesis. FBFM supplementation also promoted the enrichment of beneficial gut microbiota, notably Firmicutes and Proteobacteria, although overall α-diversity decreased. These findings demonstrate that dietary FBFM supplementation improves heat stress resilience in large yellow croaker by enhancing antioxidant capacity, optimizing energy metabolism, and modulating gut microbiota. This work highlights the potential of FBFM as a nutritional strategy to promote growth and health of marine fish under environmental stress.