Abstract: This paper demonstrates a massively parallel 3D full-wave electromagnetic field simulation program JEMS-FDTD and its application in complicated electromagnetic environment study. Two numerical examples of application are presented. The computation of radio wave propagation in actual building produces the numerical results of the propagation process of electromagnetic pulse in time domain, which can be used to analyze the characteristics of indoor radio propagation and electromagnetic environment safety. The computation of aircraft transient electromagnetic characteristics gives the transient electromagnetic field distribution inside and outside the compartments, which can be used in HIRF (High Intensity Radiation Field) protection study.