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Objective To investigate the alterations in hippocampus neuron morphology, the expression of neurogenin 2 (Ngn2) and methyl-CpG-binding protein 2 (MeCP2) in hippocampus after electromagnetic pulse (EMP) irradiation. Methods Adult healthy male SD rats were randomly divided into control group, EMP 7-day group, and EMP 14-day group (n=12). Hippocampus neuron morphology was tested by HE staining; the expression of Ngn2 and MeCP2 were measured by Western blotting and fluorescent immunohistochemistry; the protein levels of brain-derived neurotrophic factor (BDNF) and postsynaptic density protein 95 (PSD95) were measured by Western blotting. Results Compared with the control group, the number of pyramidal cells in the EMP 7-day group and EMP 14-day group was reduced, the neuron boundary was blurred, and the nuclear outline was blurred. Compared with the EMP 7-day group, the hippocampus neuron structure in the EMP 14-day group was more severely damaged. Compared with the control group, the expression of Ngn2, BDNF, and PSD95 significantly decreased, while the expression of MeCP2 increased in the EMP 14-day group and EMP 7-day group. Conclusion EMP exposure leads to the pathological damage of hippocampus neurons in rats, increases MeCP2 expression and decreases Ngn2, PSD95, BDNF expression.