<p>Ischemic stroke is one of the common causes of disability and death, and subsequent pathological processes consequent to revascularization could promote secondary tissue damage leading to neuronal death, namely cerebral ischemia and reperfusion injury. Neutrophils could invade injured brain parenchyma after vascularization and exert neurotoxicity by forming neutrophil extracellular traps (NETs). However, unwanted NETs were accumulated in the infarcted core of transient middle cerebral artery occlusion (tMCAO) rats and the mechanism is unknown. Efficient microglial phagocytosis is crucial for the homeostasis of cerebral parenchyma after stroke, and dysfunction of microglial phagocytosis of NETs were observed in the infarcted core cortex at tMCAO 1 d and the accumulation of NETs persisted to 7 d, which exerting deleterious neuronal damage after stroke. However, the detailed mechanisms underlying the dysfunction of microglial phagocytosis of NETs remained unclear. Our results further demonstrated that NLRX1 was mainly enhanced in the microglial cells in the infarcted core cortex at tMCAO 1 d and promoted galectin-3 expression on the lysosomes, facilitating the lysosomal dysfunction and impaired microglial phagocytosis via mTOR/TFEB signaling. NLRX1-silencing was able to suppress the galectin-3 intensity, inhibit the phosphorylation of mTOR and facilitate the nuclear localization of TFEB, ameliorating the lysosomal dysfunction and microglial phagocytosis of NETs. Our results uncovered the regulation of NLRX1 in the dysfunctional microglial phagocytosis of NETs and provided insights into the therapeutic potential for targeting at microglial lysosomal function in cerebral ischemia and reperfusion injury.</p>