In this paper, we present a hybrid electromagnetic bandgap (EBG) structure based on a three-hole double-layer configuration. One layer of the EBG structure is positioned on the metal, while the other is on the printed circuit board (PCB). Dispersion analyses reveal that this new compact hybrid EBG could produce a wide stopband with high in-band attenuation. To evaluate its effectiveness in mitigating signal leakage at waveguide-to-PCB interfaces and its potential application in next-generation satellite communications (Sat-Corns), we designed two EBG structures specifically for low-Earth orbit and geosynchronous orbit SatCom hybrid array antennas within the E-band (71-86 GHz). The performance of these EBG structures is evaluated in the configuration of 4 × 4 hybrid arrays. We demonstrate that the proposed hybrid EBG structures can effectively enhance power transmission and significantly reduce mutual coupling in the waveguide-to-PCB interfaces.