Cerebral ischemia/reperfusion injury (CIRI) refers to secondary damage caused by reperfusion of blood flow following ischemic stroke. Its mechanism is complex, involving mitochondrial energy metabolism disorders, Ca2+ overload, oxidative stress, apoptosis, inflammatory responses, excitatory amino acid toxicity, blood-brain barrier disruption, excessive NO synthesis, and cell necrosis etc. Mitochondrial-associated endoplasmic reticulum membranes (MAMs) are specialized regions of the endoplasmic reticulum that play crucial roles in various cellular processes, including regulation of mitochondrial morphology and activity, lipid metabolism, Ca2+ homeostasis, and cell viability. Existing research has confirmed that mitochondrial homeostasis, cell apoptosis, and endoplasmic reticulum stress are closely related to MAMs. This article summarizes the research progress on MAMs in recent years, reviews the biological functions of MAMs and the localization of tethering proteins, analyzes the signaling between mitochondria and the endoplasmic reticulum, explores the impact of MAMs tethering proteins interaction on Ca2+ signaling and cell viability during the pathophysiological process of CIRI, aiming to provide a theoretical basis for the treatment of CIRI.