Hybrid groupers have emerged as a significant aquaculture species owing to their high market value and growing demand. However, carbohydrate-rich diets pose a challenge for efficient glucose metabolism in this species. This phenomenon stems from the limited capacity of fish to effectively metabolize glucose in response to high-carbohydrate diets, resulting in persistent hyperglycemia that adversely affects growth performance. Impaired insulin sensitivity and dysfunction in insulin signaling, characterized by compromised insulin receptor function, blocked insulin cascades, and failure to activate critical signaling pathways, such as the PI3K/AKT pathway, have been identified as key factors contributing to this metabolic disorder. Therefore, this study investigated the application of metformin, a biguanide with recognized hypoglycemic properties, to ameliorate the adverse effects of high-carbohydrate diets in hybrid groupers (Epinephelus lanceolatus × E. fuscoguttatus). A total of 540 pearl gentian grouper, averaging (10.44±0.01) g, were selected and randomly distributed into six treatment groups, each consisting of three replicates with 30 fish per replicate. Six iso-nitrogenous and iso-lipid diets were formulated: A positive control (20% carbohydrate, PC), one negative control (30% carbohydrate, T0), and four experimental groups supplemented with metformin at concentrations of 0.2% (T2), 0.4% (T4), 0.6% (T6), and 0.8% (T8) relative to the negative control. The results show that the carbohydrate and metformin levels in the feed had no statistically significant effect (P＞0.05) on the feed coefficient ratio (FCR) and survival rate (SR). Notably, a high-carbohydrate diet reduced growth performance (WGR, SGR) in hybrid groupers and altered serum biochemical parameters, increasing glucose, triglycerides, and LDL. Meanwhile, decreasing insulin and HDL. Metformin supplementation mitigated these effects, improving lipid metabolism markers and partially restoring HDL levels, with optimal outcomes at higher doses. Growth and organ indices demonstrated linear or quadratic trends in response to metformin, though condition factor (CF) and alpha diversity of gut microbiota were unaffected. Metformin also modulated gut microbial composition, decreasing Proteobacteria and Photobacterium while increasing Firmicutes and Brevibacillus. In the present study, a high-carbohydrate diet inhibited growth performance, decreased insulin sensitivity, and increased the abundance of pathogenic intestinal bacteria in hybrid groupers. In the present study, the administration of a high-sugar diet augmented with 0.2% metformin altered the composition of intestinal microorganisms, thereby enhancing the disruption of glucose metabolism in the intestinal flora of groupers. This disruption is induced by a high-carbohydrate diet that promotes glycolysis and inhibits gluconeogenesis, thereby regulating glucose homeostasis. This, in turn, facilitates an improvement in the utilization rate of carbohydrates by the pearl gentian grouper.