The study investigated the impact of chlorogenic acid (CGA) supplementation in a high-fat diet (HFD) on growth, lipid metabolism, intestinal and hepatic histology, as well as gut microbiota in spotted sea bass. A total of 540 fish were fed six experimental diets, including a normal fat diet (NFD), a high-fat diet (HFD), and HFD supplemented with 100, 200, 300, and 400 mg/kg CGA (named HFD1, HFD2, HFD3, and HFD4, respectively) for 7 weeks. The results showed that HFD feeding increased growth and hepatic lipid deposition compared to that in the NFD group. Inclusion of 300 mg/kg CGA in HFD decreased the HFD-induced hyperlipemia (p < 0.05). Additionally, compared to the HFD group, the HFD4 group showed significant reductions in serum aspartate transaminase (AST) and alanine transaminase (ALT) levels as well as hepatic malondialdehyde (MDA) content, while also improving liver total antioxidant capacity (T-AOC) (p < 0.05). In the CGA-containing groups, hepatocytes were arranged more neatly than those in the HFD group, and there was a reduction in lipid deposition and hemolysis in the liver. Supplementation of CGA had effects on intestinal structure including an increase in mucosal thickness, as well as villus number and width. The diversity of intestinal flora in the CGA-containing groups was higher than those in the HFD group, and supplementation of 200 mg/kg CGA significantly increased the abundance of intestinal bacteria (p < 0.05). HFD4 feeding increased the intestinal Bacteroidetes to Firmicutes ratio and decreased the abundance of Vibrio. The highest value abundance of Actinobacteriota was found in the HFD2 group. Overall, HFD caused negative effects, and supplementation of 200-400 mg/kg CGA to HFD improved fat deposition, lipid metabolic disorders and liver and gut histology, and increased gut bacterial diversity in spotted sea bass.