Objectives To study the effects of contusion and exhaustive exercise on gene expression of MG53, PTRF, Pax7 and β-catenin in skeletal muscle of rats, and reveal the repair mechanism of skeletal muscle injury. Methods Forty-two male Wistar rats were randomly divided into 7 groups, with 6 rats in each group. All groups were euthanized at different time points after exhaustive exercise and contusion, respectively, while the control group was euthanized in resting state. The right gastrocnemius muscles were measured for mRNAs of MG53, PTRF, Pax7 and β-catenin by real time PCR. Results MG53 mRNA and PTRF mRNA of skeletal muscle in groups immediately after exhaustive exercise and after contusion increased significantly (p<0.05), while the two indices decreased constantly at 24 and 48 hours after injury with a similar change trend. Compared with the control group, Pax7 mRNA of skeletal muscle as a marker showed no significant difference in exhaustive exercise groups, but decreased at 48 hours after contusion (p<0.05). β-catenin mRNA of skeletal muscle down-regulated significantly over 24 hours after injury, then activated with an increased value at 48 hours after contusion (p<0.05). As a whole, the variations in the above indices in the contusion groups covered a wider range than in the exhaustive exercise groups. Conclusion The cytomembrane repair mechanism of MG53 and PTRF began immediately after the end of exhaustive exercise and contusion. Activation of Pax7 as the satellite cell marker took longer, and Wnt/β-catenin pathway showed first a decrease and then an increase resulting from the time-dependent gene expression during the repair of skeletal muscle injury. Level of evidence III, Therapeutic studies investigating the results of treatment.