Backgrounds: Exercise benefits nonalcoholic fatty liver disease (NAFLD), and amino acids (AAs) are close associated with the development and progression of NAFLD. However, it is unclear whether AAs profile changes following long term exercise training.Methods: NAFLD participants (n=220) were recruited and randomly assigned to control group, moderate exercise group, and vigorous exercise group with a 6-month followed-up. Clinical characteristics were carefully calculated and plasma AAs concentrations were determined using a validated ultrahigh performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method. Results: At baseline, AAs concentrations were close associated with clinical characteristics in NAFLD, particularly, the sum of branched chain amino acids (BCAAs) were positively associated with intrahepatic triglyceride (IHTG) content (r=0.18, P=0.007). After 6 month exercise intervention, IHTG content was reduced by both exercise intensities without a significant difference (P=0.45). Compared to control, several AAs concentrations altered, and different exercise intensity showed inversely impact on histidine, serine, glutamine, valine, tyrosine and tryptophan concentrations changes, particularly, moderate exercise was much more efficient on BCAAs decreasing than vigorous exercise with a significant difference (P=0.0008). Conclusions: Several AAs were close associated with IHTG content in NAFLD patients, and 6 month moderate exercise was more efficient on AAs concentrations alteration, especially BCAAs decreasing than vigorous exercise. Trial registration number: NCT01418027