Generally, most of the electronic equipments need a metallic enclosure in order to mechanically protect and to electrically shield the interior printed circuit boards (PCBs) and subsystems. But in the practical situations, the apertures or slots of various forms are essential parts of the shielding enclosure for heat dissipation, CD-ROMs, connectors, I/O cabling and so on. The performance of shielding enclosures for high-speed digital systems is compromised by those inevitable discontinuities on enclosure. To minimize the electromagnetic interference and susceptibility risk by those discontinuities, the shielding enclosures with apertures should be designed based on the thorough analysis about the electromagnetic coupling mechanism through apertures. In this paper, the effect of apertures on shielding effectiveness of the enclosure is studied with the finite-difference time-domain (FDTD) method. And the simulated SE data are verified numerically and experimentally. Good agreements are seen. Also several guidelines on the apertures design of shielding enclosure are verified with the numerical methods.