This trial was conducted to assess the effects of different levels of dietary fish oil on growth performance, hepatic health, nonspecific immune responses, and intestinal microbial community of Amur grayling (Thymallus grubii). Five isonitrogenous diets containing 60 (6FO), 90 (9FO), 120 (12FO), 150 (15FO), and 180 g/kg (18FO) fish oil were fed to triplicate groups of 60 fish per tank for 8 weeks, respectively. The results revealed that specific growth rate (SGR) and weight gain (WG) of fish in the 15FO group were significantly greater than those in the 6FO group (p < 0.05). Somatic indices and whole‐body lipid levels were positively correlated with increases in dietary fish oil levels. Trypsin and lipase activities in 15FO and 18FO groups were significantly higher than those in the 6FO and 9FO groups (p < 0.05). The activities of intestinal catalase (CAT) and liver superoxide dismutase (SOD), CAT, lysozyme (LZM), alkaline phosphatase (AKP), and acid phosphatase (ACP) improved significantly as the dietary lipid content increased to 185.3 g/kg and decreased thereafter (p < 0.05). The lipid metabolism‐related genes peroxisome proliferator‐activated receptor gamma (PPARγ) and carnitine palmitoyltransferase 1A (CPT1A) were significantly downregulated and upregulated (p < 0.05), respectively, in the 15FO group. Immune‐related genes in the liver and intestine, such as interleukin (IL‐8), were significantly upregulated in the 15FO group (p < 0.05). The liver sections from 18FO group presented more numerous and larger lipid vacuoles. Both low‐ (6FO) and high‐lipid (18FO) diets reduced the relative abundance of intestinal Lactococcus. The relative abundances of intestinal Staphylococcus and Bacillus (mainly Bacillus anthracis) increased in the low‐lipid diet group and that of Pedobacter increased in the high‐lipid diet group. Second‐order polynomial analysis of WG and the feed conversion ratio (FCR) for varying levels of dietary lipid revealed that a range of 194.76–198.90 g/kg dietary lipid was optimal for the growth and health of Amur grayling.