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BACKGROUND: Different intensities of exercises make different effects on human body, and the changes of skeletal muscle after exercise remain unclear. Physical change of human body during exercise is a hotspot. METHODS: The study was approved by the Laboratory Animal Ethical Committee of Beijing Sport University. Twenty-four healthy male Sprague-Dawley rats aged 8 weeks were randomly divided into three groups: control, moderate-intensity exercise (5°, 15 m/min, 1 hour, 60% VO2max) and high-intensity exercise (5°, 35m/min, 20 minutes, 85% VO2max) groups (n=8/group), 6 times weekly. The rat soleus and gastrocnemius were removed to measure the wet weights. The cross-sectional area of muscle fiber was detected by immunofluorescence. The protein expression levels of BNIP3, p62 and LC3 in the soleus and gastrocnemius were detected by western blot assay. RESULTS AND CONCLUSION: (1) The wet weight of gastrocnemius in the exercise groups was significantly lower than that in the control group (P < 0.01). (2) The cross-sectional area of gastrocnemius fiber in the exercise groups was significantly less than that in the control group (P < 0.01), and the cross-sectional area of soleus fiber in the exercise groups was significantly more than that in the control group (P < 0.01 ). (3) The moderate-intensity exercise induced increased mitophagy, and the expression level of BNIP3 and LC3-II/LC3-I were up-regulated (P < 0.05), while p62 was down-regulated (P < 0.05) compared with the control group. The expression level of LC3-II/LC3-I in the high-intensity exercise group was higher (P < 0.05), but the expression level of p62 was lower than that in the moderate-intensity exercise group and the expression of BNIP3 was decreased (P < 0.05). (4) To conclude, 4-week moderate-intensity exercise can promote the removal of damaged mitochondria and maintain skeletal muscle function by increasing BNIP3-regulated mitophagy in skeletal muscle. In high-intensity exercise, the level of autophagy is higher, but will cause harmful effect on skeletal muscle. [ABSTRACT FROM AUTHOR]