The key target and regulatory mechanism of electroacupuncture of Zusanli (ST36) on extensor longus muscle injury in a jumping rat model were investigated. To this end, 24 female SD rats were randomly divided into the following four groups: no-treatment control group (NON), 6-week jumping group (J6O), electroacupuncture group after 6-week jumping (J6A), and natural recovery group after 6-week jumping (J6N). After 6 weeks of jumping, in the electroacupuncture group (J6A), electroacupuncture stimulation was applied at Zusanli(ST36) for 20 min per day over the course of 5 days. In the natural recovery group (J6N), rats were fastened with a special apparatus without electroacupuncture stimulation for 20 min at the same time. Transmission electron microscopy, transcriptome sequencing and analysis, Western blotting assay and immunofluorescence staining were performed at the end of our experiment. The recovery effect of J6A rats was more obvious than that of J6N rats and J6O rats as indicated by changes of infiltration of inflammatory cells and morphological structure. Notably, the morphological structure of J6A rats was closer to NON rats in the observation of transmission electron microscopy. CISH/STAT3 regulation was identified by mRNA-seq. The pro-inflammatory response to STAT3 activation was alleviated through up-regulating the expression of CISH protein in J6A rats relative to J6O rats. The level of BAX was decreased and the level of Bcl-2 level was increased in J6A rats relative to J6O rats. Moreover, when compared to J6N rats, the level of Bcl-2 was significantly up-regulated in J6A rats. Increased caspase-3 expression but decreased CDKN2α expression was shown in J6A rats relative to NON rats. These results indicate that the potential mechanism underlying electroacupuncture stimulation of Zusanli (ST36) in repairing the injured extensor digitorum longus following overused jumping may be attributed to CISH/STAT3 regulation of proteins associated with inflammation, apoptosis, and proliferation.