Objective <p>Our research aims to explore the effects of different exercise on liver function and bile acid in patients with non-alcoholic fatty liver disease (NAFLD), to identify the most beneficial exercise modalities for patients with NAFLD.</p> Design <p>Participants were randomly divided into four groups: control group, aerobic training group, resistance training group, and aerobic training combined with resistance training group. Participants underwent assessments of body shape, blood lipid, glucose levels and liver function biochemical parameters. Their bile acid levels were measured using the LC–MS/MS system. Changes in these parameters before and after the intervention and differences between groups were analyzed.</p> Results <p>Participants in the AT group showed significant improvements in liver function parameters. Additionally, levels of total bile acids and ursodeoxycholic acid significantly increased. The RT group and AT + RT group also showed improvements in body shape and liver function parameters, but the improvements in these groups were not as pronounced as those in the AT group.</p> Conclusions <p>Aerobic exercise is the most beneficial modality for young patients with NAFLD, as it significantly improves body shape and liver function while also reducing blood lipid and glucose levels.</p> Trial registration <p>Clinical trial number NCT06338449, registered on March 22, 2024.</p>