In recent times, due to the high operating frequency and low operating voltage of modern electronic devices, intended electromagnetic interference (IEMI) has been the cause of increasing damage. In particular, targets with precision electronics such as aircrafts or missiles have shown that a high-power microwave (HPM) may cause malfunction or partial destruction of the GPS or the avionic control system. Analysis of the effects of IEMI requires electromagnetic numerical analyses. However, there are limitations to conventional numerical techniques, such as the finite element method, method of moment, or finite difference time domain method, due to the complexity and large electrical length of a real target system. In this paper, we proposed a new cylindrical mode matching (CMM) technique to analyze IEMI of the generic missile (GENEC) model, which is a hollow metal cylinder with multiple apertures. Using the CMM, we can quickly analyze the effect of the IEMI inside the GENEC model from 1.7 to 2.5 GHz. The results were compared with those of the measurements and, for verification, with the FEKO, a commercial software program developed by Altair Engineering, and showed good agreement. In this paper, the electro-optic (EO) probe was used to measure the electric field inside the GENEC model.