With the increasing incorporation of plant-based ingredients into the grouper diet, the issue of aflatoxin B1 (AFB1) contamination in the diet has become a significant concern. In this study, the negative effects of AFB1 on the growth and liver health of hybrid grouper (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂) were investigated in the context of growth, liver histology, serum biochemical indices, and integrated transcriptomic and metabolomic data. A total of 540 healthy hybrid groupers, initially weighing 11.59 ± 0.03 g, were randomly divided into six groups (three replicates of 30 fish each): the Control group was fed a basal diet, and the experimental groups were supplemented with 7 (AF7), 30 (AF30), 111 (AF111), 445 (AF445) and 2230 μg/kg AFB1 (AF2230) in the basal diet respectively, for 56 days. Groups Control, AF445, and AF2230 were selected for subsequent histological, muscle fatty acid, and transcriptomic and metabolomic analyses based on the results of hybrid grouper growth and serum biochemical indices. Compared to the Control group, both whole-body crude lipid and muscle crude lipid contents showed significant decreases in the AF2230 group (P < 0.05), while only muscle crude lipid content showed a significant decrease in the AF445 group (P = 0.001). Liver damage was seen in the histology of the liver of AF445 and AF2230 groups. Muscle fatty acid results showed that the addition of 445 and 2230 μg/kg AFB1 to the ration increased saturated fatty acids and monounsaturated fatty acids and decreased polyunsaturated fatty acids and highly unsaturated fatty acids in muscle (P < 0.05). Transcriptome analyses revealed multiple metabolic pathways associated with AFB1 metabolism, and metabolomics analyses further confirmed changes in the activity of these pathways. The results of the combined transcriptomic and metabolomic analyses indicated that AFB1 causes liver injury mainly by affecting liver retinol metabolism, metabolism of xenobiotics by cytochromes P450, drug metabolism-cytochromes P450 and biosynthesis of unsaturated fatty acids. In conclusion, dietary AFB1 levels above 445 μg/kg resulted in growth inhibition, liver injury, liver AFB1 accumulation, and reduced muscle polyunsaturated fatty acid content in grouper, thereby affecting muscle quality. This study provides novel insights into the detrimental effects of AFB1 on aquatic species and contributes to the scientific basis for the health and sustainability of aquaculture practices.