In order to prevent cardiac pacemakers from malfunctioning caused by electromagnetic (EM) wave, as one of the solutions to the problem of pacemaker malfunctioning, we can use a shielding material to decrease the EM wave intensity. For the effective suppression of the EM wave including a complicated enclosure or a human body, it is desirable to solve for the EM wave propagation by using numerical analysis. We introduce the transmission coefficient when an EM wave is incident into a multi-layered material with an arbitrary direction into the FDTD method. This realizes three-dimensional numerical analysis of a thin shielding material as a method to solve the EM wave transmission problem, which has been conventionally considered difficult. We use a phantom model, a dummy model of a cardiac pacemaker wearer, to analyze the EM wave shielding effectiveness of the shielding clothes. The analytical result agrees fairly well with the experimental result, which verifies the validity of the developed method. As for the effect of the aperture of the shielding clothes, the EM wave coming around from the apertures is found to be larger in amount than the EM wave transmitted through the clothes, which suggests that the aperture causes the SE to decrease largely.