Heart failure (HF) is the terminal stage of a variety of cardiovascular diseases. Mitochondrial dysfunction is a key factor in the development of HF. Yang deficiency and water stagnation is the core TCM pathogenesis of HF. Mitochondrial dysfunction leads to energy deficiency, produces reactive oxygen species (ROS), and accelerates cardiomyocyte injury, which is similar to the pathogenesis of "yang deficiency" in TCM; mitochondrial dysfunction leads to water and sodium retention and edema, which is consistent with the TCM pathogenesis of "water stagnation". Mitochondrial dysfunction may explain the syndrome of "yang deficiency and water stagnation" in HF at the micro level, while the method of warming yang and diuresis or regulating mitochondrial function through multiple targets can improve HF. This provides a new research idea and theoretical basis for the treatment of HF with integrated traditional Chinese and Western medicine.