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Background: To investigate the effects of different levels of microwave radiation on learning and memory in Wistar rats and explore the underlying mechanisms of N-methyl-D-aspartate receptor (NMDAR/NR) and Brain-derived neurotropic factor (BDNF); Methods: A total of 140 Wistar rats were exposed to microwave radiation levels of 0, 10, 30 or 50 mW/cm² for 6 min. Morris Water Maze Test, high-performance liquid chromatography, Transmission Electron Microscope and Western blotting were used; Results: The 30 and 50 mW/cm² groups exhibited longer average escape latencies and fewer platform crossings than the 0 mW/cm² group from 6 h to 3 d after microwave radiation. Alterations in the amino acid neurotransmitters of the hippocampi were shown at 6 h, 3 d and 7 d after exposure to 10, 30 or 50 mW/cm² microwave radiation. The length and width of the Postsynaptic density were increased. The expression of NR1, NR2A and NR2B increased from day 1 to day 7; Postsynaptic density protein-95 and cortactin expression increased from day 3 to day 7; BDNF and Tyrosine kinase receptor B (TrkB) expression increased between 6 h and 1 d after 30 mW/cm² microwave radiation exposure, but they decreased after 50mW/cm² exposure. Conclusions: Microwave exposure (30 or 50 mW/cm², for 6 min) may cause abnormalities in neurotransmitter release and synaptic structures, resulting in impaired learning and memory; BDNF and NMDAR-related signaling molecules might contribute differently to these alterations.