Ischemic stroke (IS) is a common cerebrovascular disease with a complex pathogenesis and a prolonged, refractory clinical course. Under the guidance of the Traditional Chinese Medicine (TCM) theory of "Qi Deficiency and Stasis," it can be characterized as a syndrome of deficiency in origin and excess in manifestation, where "Qi Deficiency" is the root and "Stasis" is the manifestation. Modern research has found that mitophagy, as a key process in maintaining cellular homeostasis, is extensively involved in the regulation of IS. Its functional state aligns with the pathological changes described in the "Qi Deficiency and Stasis" theory. Therefore, this article systematically explores the intrinsic relationship between the "Qi Deficiency and Stasis" theory and mitophagy in the occurrence and progression of IS, while proposing therapeutic strategies. By establishing a bridge between TCM pathogenesis and modern biological mechanisms, it provides a new theoretical basis and research direction for targeting mitophagy in the prevention and treatment of IS based on the "Qi Deficiency and Stasis" theory.