Cultured Epinephelus akaara generally suffers from slow growth and decreased skin beauty. It has been previously verified that astaxanthin, as a feed additive, has a positive effect on the coloring and antioxidant capacity of E. akaara. Other studies have found that astaxanthin can induce autophagy to regulate the body's lipid metabolism and promote liver and intestinal health functions. Therefore, this study conducted a three-month experiment on E. akaara fed with astaxanthin supplemented with different concentrations (0, 100, 200, 400, and 800 mg/kg). The effects of astaxanthin on HSI, hepatocyte and intestinal epithelial cell structure and autophagy of E. akaara were investigated by measuring hepatosomatic index (HSI) and using transmission electron microscopy (TEM). The regression analysis model showed that with the increase of astaxanthin supplemental level, liver HSI of E. akaara showed a decreasing trend, and HSI in AST800 group was significantly lower than that in control group (P<0.05). The ultrastructure of liver showed that the area of hepatocytes in AST800 groupwas significantly smaller than that of the control group (P<0.05), and the number of autophagosomes, autophagolysosomes and mitochondria increased significantly (P<0.05), while the number and area of lipid droplets were significantly decreased (P<0.05). The presence of small clumpy lipid droplets and mitochondria in the autophagosome contents suggested the occurrence of lipid droplet autophagy and mitochondrial autophagy. The intestinal ultrastructure showed that the number of autophagosomes, autolysosomes and mitochondria in intestinal mucosal epithelial cells of AST800 group was significantly increased compared with the control group (P<0.05), and the microvilli were more densely arranged, and the structure of tight junction between cells became longer. Studies have shown that adding astaxanthin to the diet can induce autophagy, regulate cellular lipid metabolism, reduce HSI, phagocytic mitochondria with abnormal structure, inhibit oxidative stress, and promote intestinal barrier function by regulating cell tight junction. In conclusion, autophagy plays an important role in astaxanthin regulation of liver lipids and promotion of intestinal barrier function in E. akaara, which is beneficial to its physiological activities. At the same time, the results of this study suggest that lipid autophagy may be a new target for astaxanthin to improve the accumulation of excess fat in the liver caused by dietary diet, and provide experimental basis for further development and utilization of astaxanthin in fish feed.