This study investigates the mechanisms and target sites of Renshen (Ginseng Radix et Rhizoma)-Danshen (Salviae Miltiorrhizae Radix et Rhizoma) (RSDS) in regulating myocardial ischemia-reperfusion injury (MIRI) via the silent information regulator 3 (SIRT3)/peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α)/voltage-dependent anion-selective channel 1 (VDAC1) signaling pathway. A rat MIRI model was established and randomly divided into control, model, fosinopril, and low-, medium-, and high-dose RSDS groups. Cardiac function, cell apoptosis, and myocardial fibrosis were assessed using cardiac ultrasound, TUNEL staining, hematoxylin-eosin (HE) staining, and Masson staining. Serum factors and the expression of key proteins and genes, such as SIRT3, PGC-1α, and VDAC1 in myocardial tissue, were analyzed using ELISA, Western blot, and RT-qPCR to investigate the underlying mechanisms through the SIRT3/PGC-1α/VDAC1 signaling pathway. The experimental results showed that, compared with the model group, RSDS significantly improved cardiac function, with the high-dose group exhibiting the most pronounced cardioprotective effect, including increased left ventricular ejection fraction (LVEF), decreased left ventricular end-systolic diameter (LVESD), and increased left ventricular fractional shortening (LVFS). TUNEL staining demonstrated that RSDS reduced myocardial cell apoptosis, and Masson staining indicated that RSDS significantly alleviated myocardial fibrosis. Serum levels of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), C-reactive protein (CRP), and creatine kinase-MB (CK-MB) were significantly decreased, while superoxide dismutase (SOD) levels were significantly increased, suggesting strong anti-inflammatory and antioxidant effects. Western blot and RT-qPCR analyses demonstrated that RSDS improved mitochondrial function, inhibited oxidative stress, and protected myocardial cells by regulating the SIRT3/PGC-1α/VDAC1 signaling pathway. In conclusion, RSDS significantly ameliorates cardiac dysfunction induced by MIRI through regulation of the SIRT3/PGC-1α/VDAC1 signaling pathway, reducing myocardial apoptosis, fibrosis, and inflammation.