Objective To investigate the effects of moderate aerobic exercise and high intensity intermittent exercise on myocardial mitochondria autophagy in mice with non-alcoholic fatty liver disease and its possible mechanism. Methods Forty 3-week-old male C57BL/6J mice were randomly divided into normal feeding group (Chow group, n=10) and high fat feeding group (HFD group, n=30). At week 18, those whose body weight in HFD group exceeded 20%~30% (including 20%) of the ordinary diet group were judged as obese mice (n=26). Two mice were randomly selected for liver oil red O staining to confirm the successful establishment of NAFLD mouse model. Sixteen NAFLD mice were randomly selected and divided into moderate intensity aerobic exercise group (MICT group) and high intensity intermittent aerobic exercise group (HIIT group), with 8 mice in each group. The two groups were given exercise training for 8 weeks, respectively, and the samples were weighed after intervention. Masson staining was used to observe myocardial fibrosis. The ultrastructure of myocardial cells was observed by transmission electron microscopy. Mitochondrial autophagy and mitochondrial biogenesis were detected by Western Blot. Results ⑴ Compared with Chow group, body weight and heart index in HFD group were significantly increased and decreased. Compared with HFD group, the body weight of MICT and HIIT group increased significantly, and the heart index of MICT group increased. (2) Masson results showed that compared with Chow group, the content of collagen fibers in myocardium in HFD group was significantly increased, and the myocardial fibers were disorganized and broken under electron microscope. The morphology of myocardium was disorganized, mitochondria were swollen, crists were broken and blurred, and lipid droplets were included. Compared with HFD group, the myocardial collagen fiber content in MICT and HIIT groups was significantly reduced, the myocardial fiber arrangement was slightly recovered under transmission electron microscopy, the Z-line was clearly visible, the degree of mitochondrial degeneration was slightly improved, and the lipid droplets were also slightly reduced. Among them, the improvement effect of MICT group on the cardiac tissue structure was better than that of HIIT group. (3) Western Blot results showed that compared with Chow group, the expression levels of PINK1 and Beclin1 in myocardial tissue of HFD group had no significant changes, while the expressions of Parkin, LAMP1 and PGC-1α were significantly decreased (p<0.01). p62 protein expression and LC3-II/LC3-I ratio were significantly increased (p<0.05, p<0.01); Compared with HFD group, the expression levels of PINK1 and Beclin1 in MICT and HIIT groups were not significantly changed, while the expression of PGC-1α was up-regulated, and the expressions of Parkin and LAMP1 in MICT group were significantly increased (p<0.05). p62 protein expression and LC3-II/LC3-I ratio were significantly decreased (p<0.05, p<0.01), Parkin and LAMP1 expression levels were up-regulated, LC3-II/LC3-I ratio and p62 protein expression were significantly decreased in HIIT group (p<0.05, p<0.01). Conclusion Different forms of aerobic exercise can effectively ameliorate myocardial structural and functional injury in NAFLD mice, which may be through stimulating the autophagy flux of mitochondria in cardiomyocytes, activating autophagy and restoring the normal autophagy function of cells, so as to ameliorate myocardial cell damage, and moderate continuous aerobic exercise has better improvement effect.