A compact common-mode suppression filter is proposed by employing the modified ground structure (MGS) for high speed digital interconnects using differential signals on the multi-layered printed circuit board (PCB). It consists of two folded U-shaped slot resonators and arranged via-holes. It has compact size of 0.073λg × 0.225λg when the center frequency is 5.2 GHz. A test board is fabricated on four-layered PCB through an optimizing process for verifying effects of the proposed MSG structure. The proposed MGS can suppress the common-mode noise over 10 dB from 4.34 to 6.07 GHz in the frequency domain and over 52% of amplitude in the time domain. Furthermore, the proposed filter still keeps good signal integrity characteristics with regard to the insertion loss of differential-mode signals. It is clear that the proposed filter structure can apply to the multi-layered PCB of commercial mobile devices due to its compact size and have some advantages such as wide bandwidth, gigahertz frequency range, low cost, and PCB embedded design.