The present study was conducted to investigate the possible lipid metabolism regulatory function of fenofibrate in obscure puffer fed with different dietary lipid levels. Obscure puffer were fed a low‐fat diet (LFD, 38.0 g/kg fat), medium‐fat diet (MFD, 132.0 g/kg) or high‐fat diet (HFD, 223.0 g/kg) for 10 weeks, and then fed diets supplemented with or without fenofibrate for 2 weeks. The results demonstrated that the final mean weight, hepatosomatic index (HSI), viscera index (VSI) and serum triglycerides (TG), cholesterol (CHO) levels increased, and the expression of pparα and some lipolysis‐related genes were up‐regulated as dietary lipid level increased. Dietary fenofibrate supplementation had no significant lipid‐lowering effect on fish fed with low or medium‐fat diets but significantly induced the expression of acox1. In contrast, fenofibrate treatment exhibited lipid‐lowering effect on obscure puffer fed with high‐fat diets, including significantly decreased the whole body crude lipid content, serum TG, CHO contents and hepatocyte lipid droplets size. Furthermore, dietary fenofibrate treatment significantly increased the expression of genes related to lipolysis (pparα, acox1, cpt1 and lpl) and lipogenesis (fas and pparγ) when fish were fed with high‐fat diets. Taken together, our present study suggested that the lipid‐lowering effects of fenofibrate were affected by the nutritional background of obscure puffer.