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Objective To determine the effect of the autophagy inhibitor, 3-methyladenine (3-MA), on cognitive function changes, microglia activity, neuronal apoptosis, and inflammation in rats following radiation-induced brain injury. Methods The following groups were established: control, model, and 3-MA. A rat model of radiation-induced brain injury was generated with a medium dose of X-rays. A Morris water maze was used to observe the cognitive function of the rats. H&E staining was used to observe the pathological changes in the hippocampus. The morphological and quantitative changes of neuronal nuclear (NeuN)-positive neurons and Iba-1-positive microglia in the ipsilateral hippocampus were analyzed by immunohistochemistry. Western blot analysis was done to measure the changes of NeuN ionized calcium binding adapter molecule 1(Iba-1) and apoptosis-related proteins. Immunofluorescence staining of Iba-1 and Microtuble-associated protein light chain 3 (LC3) was done to evaluate the changes in microglia autophagy. TUNEL staining was used to detect apoptosis in the hippocampus. Enzyme-Linked Immunosorbent Assay was used to detect the levels of TNF-α and IL-6 as a measure of the inflammatory response in the hippocampus. Results After irradiation, the nucleus of the neurons in the hippocampus was constricted, the pyramidal tract structure was disordered, neuronal apoptosis was increased ( P < .001), the expression of microglia increased ( P < .01), autophagy was increased ( P < .05), and conversion of microglia to the M2 type increased ( P < .05). After 3-MA administration, the level of autophagy decreased ( P < .05), the damage to the hippocampal region was reduced, neuronal apoptosis decreased ( P < .01), and the activity of the microglia decreased ( P < .01). Conclusion Radiation can active the Microglia. 3-MA inhibits autophagy and excessive activity in microglia, and promotes the conversion of microglia from the M1 to the M2 type, thereby promoting the recovery of brain tissue following radiation exposure.