MAPKK4 has been implicated in the pathological mechanisms underlying myocardial and vascular injury, specifically influencing endothelial cell damage and programmed cell death via subcellular pathways. Nevertheless, the regulatory role of MAPKK4 in coronary microvascular injury following myocardial infarction remains unconfirmed, and the exploration of targeted mitochondrial protective therapeutic agents remains unaddressed. In light of this gap, we established a MAPKK4 gene-modified mouse model of ischemia-reperfusion injury and employed Buyang Huanwu decoction (BYHW), a traditional cardiovascular therapeutic formula, to assess its efficacy in treating coronary microvascular injury post-ischemia-reperfusion. The study aimed to elucidate the mechanism by which BYHW mitigates coronary microvascular injury induced by ischemia-reperfusion through the attenuation of endothelial cell apoptosis. Experimental outcomes revealed that high-dose BYHW significantly ameliorated coronary microvascular injury post-ischemia-reperfusion, restoring the structural integrity of the coronary microvasculature and reducing inflammation and oxidative stress. Contrarily, in transgenic mice overexpressing MAPKK4, BYHW intervention failed to attenuate microvascular inflammation and oxidative stress. To further investigate, we simulated hypoxia/reoxygenation injury in vascular endothelial cells using a MAPKK4-related cellular gene modification model. The results indicated that BYHW attenuates inflammatory damage and enhances the viability of vascular endothelial cells following hypoxic stress, inhibiting apoptosis via the mitochondrial pathway. However, overexpression of MAPKK4/p38 negated the therapeutic effects of BYHW, showing no impact on endothelial cell apoptosis and oxidative stress under hypoxic conditions. Molecular interaction studies confirmed that the active components of BYHW, Astragaloside IV and Ligustrazine, interact with the MAPKK4/P38 axis.