The rapid development and industrialization of 5G communication technology has brought big challenges to the electromagnetic shielding design of electronic systems. Electromagnetic waves operating above 24 GHz in 5G communication can easily couple into the electronic systems through various vent apertures/holes on shielding enclosures. It undoubtedly degrades the system performance. To solve this problem, an electromagnetic shielding structure based on Frequency Selective Surface(FSS) with vent holes through substrate is proposed. The proposed FSS structure meets the requirements of electromagnetic shielding at 28 GHz band without affecting the ventilation. The optimally designed FSS structure through a number of full-wave simulations achieves Shielding Effectiveness(SE) greater than 30 dB at 28 GHz with a bandwidth over 2 GHz. Moreover, the proposed FSS-based shielding structure is not sensitive to the TE or TM polarization of electromagnetic wave in the incident angle range from 0°to 60°.