In the present study, juvenile hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) were intraperitoneally injected with taurocholic acid (I-TCA), obeticholic acid (FXR agonist, I-T747), guggulsterone (FXR antagonist, I-TGU), SBI-115 (TGR5 antagonist, I-TSBI), and INT-777 (TGR5 agonist, I-T777), respectively. The results showed that the fish injected with 50 mg kg−1 TCA three times during a 144 h period exhibited significantly lower hepatic lipid accumulation, compared to other concentrations and periods. Compared to the I-TCA group, the I-T747 treatment significantly increased the activities of hepatic adipose triglyceride lipase (ATGL) and carnitine palmitoyltransferase 1 (CPT1), as well as the expression of lipolysis and fatty acid uptake genes, while significantly decreased the conten of hepatic crude lipid, the activity of CPT1, and the expression of lipogenesis genes. Meanwhile, the I-TGU treatment significantly increased hepatic lipid deposition and the expression of lipogenesis genes. Compared to the I-TCA group, the I-T777 treatment did not significantly affect the parameters related to lipid deposition, but it significantly decreased the activities of acetyl-CoA carboxylase (ACC), CPT1, and fatty acid synthase (FAS), while significantly increasing the activity of ATGL and the expression of lipolysis and fatty acid uptake-related genes. Meanwhile, the I-TSBI treatment significantly increased the hepatic lipid accumulation, the activities of ACC, CPT1 and FAS, and the expression of lipogenesis and lipogenic transcriptional factors genes. In conclusion, activation of the FXR protected against the hepatic lipid accumulation by enhancing the lipolysis, while inhibition of FXR or TGR5 induced the hepatic lipid accumulation by enhancing the lipogenesis in hybrid grouper.