To investigate the effects of organic selenium (L-selenocystine, L-selenomethionine, and L-selenomethylcysteine) on non-alcoholic fatty liver disease (NAFLD), the NAFLD mice model with hepatic steatosis and fibrosis was established via feeding with a Western diet and CCl₄ injection. Compared with the model group, the intervention groups with organic selenium experienced a reduction in hepatic 5-hydroxytryptophan (5-HT) contents and downregulation in the expression of tryptophan hydroxylase 1 (TPH1) and 5-HT receptor 2A/2B/3A. Similar results were observed on TPH1/5-HT in the duodenum. In addition, organic selenium decreased the bile acid (BA) concentrations in gut contents, downregulated the expression of hepatic CYP7A1, and upregulated the expression of hepatic Farnesoid X‐activated receptor (FXR). In conclusion, our findings suggest that organic selenium ameliorates NAFLD through 5-HT/BA enterohepatic circulation in mice with NAFLD.