Mitochondrial autophagy is a unique mechanism that selectively clears dysfunctional or excess mitochondria, closely related to Alzheimer’s disease (AD), which is characterized by aggregated neurotoxic proteins and dysfunctional mitochondria. Numerous recent studies have confirmed that traditional Chinese medicine can have significant therapeutic effects against AD, and its advantages including multi-target, multi-pathway, and multi-action mechanisms have become an important component of AD research. Chinese medicine formulas and monomeric active ingredients, such as Jiannaoyizhi Fang, Danggui Shaoyao Tang, alkaloids, and flavonoids, can regulate mitochondrial autophagy-related signaling pathways and targets, inhibit neuronal mitochondrial autophagy defects, and play a neuroprotective role. This review elaborates on the basic process of mitochondrial autophagy and its related signaling pathways and molecular mechanisms in the pathogenesis of AD, and considers the latest research progress on the use of traditional Chinese medicine to improve AD by regulating mitochondrial autophagy, to provide ideas and references for future basic research and clinical treatment.