Abstract: When strong electromagnetic pulse propagates in the atmosphere, it will lead to ionization of atmospheric molecules, and at the same time, the ionized gas will react on the electromagnetic wave propagation, so the propagation state is a dynamic real-time propagation process. To accurately simulate this, physical processes such as electromagnetic wave propagation, atmospheric ionization and charged particle movement need to be comprehensively considered. In order to solve the problem, Maxwell equation, plasma equation and magnetohydrodynamics equation should be combined to construct multi-physical field analysis equations, and the atmospheric ionization, diffusion, attachment, recombination and other physical effects during the propagation of strong electromagnetic pulse should be considered. In this paper, a dynamic simulation model is built based on three-dimensional finite difference time domain (FDTD) method, and the propagation process of strong electromagnetic pulse in atmosphere is simulated in real time, also, the effect of macroscopic atmospheric ionization is analyzed.