The effect of electroacupuncture PC6 (Neiguan) combined with puerarin nanocrystal preparation (PUE-NP) on myocardial injury and autophagy in a rat model with myocardial ischemia was explored in this study. PUE-NPs were first prepared, and there was an analysis on the fourier transform infrared spectroscopy (FTIR), particle size distribution of nanocrystalline preparation, Zeta potential, and X-ray diffractometry (XRD) characterization, so as to analyze the difference in the in vitro cumulative release rate of PUE and PUE-NPs. Secondly, Sprague-Dawley (SD) rats were taken as the subjects investigated. Besides, they were divided randomly into a sham surgery group (Sham), a myocardial ischemia model group (Model), an electroacupuncture Neiguan acupoint pretreatment model group (EA+M), an electroacupuncture Neiguan acupoint pretreatment combined with PUE treatment model group (EA+PUE+M), and an acupuncture Neiguan point pretreatment combined with PUENPs treatment model group (EA+PUE-NPs+M). Then, the rats were treated with abdominal anesthesia, and their serums were extracted to detect the differences in serum creatine kinase MB isoenzyme (CK-MB) and lactate dehydrogenase (LDH) concentrations. After the rats were sacrificed, myocardial tissues were taken out, and the Western blot, hematoxylin-eosin (HE) staining, and terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) staining were employed to detect apoptosis index, pathological changes of myocardial tissue morphology, and expression differences of autophagy-related protein, such as Beclin-1, LC3, and mammalian target of rapamycin (mTOR). It was found that the average particle size of PUE-NPs was 155.9±17.3 nm, and the average Zeta potential was −15.3±2.1 mV. FTIR and XRD maps displayed that PUE-NPs nanoparticles were successfully prepared, and had a longer lasting in vitro release rate compared with PUE bulk drugs. The results of animal experiments indicated that the myocardial infarction area, serum LDH and CK-MB concentration, and myocardial cell apoptosis index, LC3II/I ratio, mTOR phosphorylation level, and Beclin-1 protein expression level of rats from the EA+M group, EA+PUE+M group, and EA+PUENPs+ M group reduced sharply compared with the model group (P < 0.05). Compared with the EA+M group, the above indicators of rats from the EA+PUE+M group and EA+PUE-NPs +M group dropped steeply (P < 0.05). Besides, the above indicators of rats from the EA +PUE-NPs+M group were lower obviously than those indicators of the EA+PUE+M group (P < 0.05). In conclusion, the above results revealed that the combination of electroacupuncture PC6 (Neiguan) and PUE preparation could improve myocardial cell apoptosis and autophagy levels in rats with myocardial ischemia, while the improvement effect of combining PUE-NPs was more marked.