Alzheimer’s disease (AD), a prevalent neurodegenerative disorder, is marked by the progressive decline in memory and cognitive function. Despite significant research efforts in the field of AD, effective therapeutic drugs for its prevention and treatment remain elusive. Consequently, a more comprehensive understanding of the molecular mechanisms underlying the pathological processes of AD is crucial for the development of novel therapeutic strategies. Mitophagy, the selective degradation of mitochondria through autophagy, is an essential mechanism for maintaining mitochondrial homeostasis in terms of both quantity and quality. It plays a pivotal role in various cellular processes, including differentiation, inflammation, and apoptosis. Recent studies have increasingly demonstrated that mitophagy is extensively characterized in AD and may represent a novel therapeutic strategy for its treatment. The distinctive properties of natural plant products (NPPs) confer significant research potential and developmental value, making them a vital resource for novel drug discovery. This study investigates the mechanistic hypothesis concerning the relationship between mitophagy and AD pathology. Furthermore, this review provides a comprehensive analysis of the application of PNPs in the prevention and treatment of AD through the regulation of mitophagy, thereby presenting novel perspectives for the exploration of AD prophylaxis and treatment.