In this study, a novel flow control scheme characterized by active suction through the structured porous surfaces on the side-walls of a square cylinder is introduced and experimentally investigated to control the shear-layer separation and dynamic wake flows. The Reynolds number (Re) is about 1.05 × 104, given the incoming flow speed and diameter of the square cylinder test model. 55 pores are regularly arranged on the top and bottom side-walls of the square cylinder to form communicating channels for the distributed suction flow. In the wind tunnel experiment, a high-speed particle image velocimetry (PIV) system is used to measure the flow field, and then a proper orthogonal decomposition (POD) method is adopted to obtain dynamic patterns of the wake flow. The experimental results demonstrated that the control effects are closely related with the dimensionless suction momentum coefficient Cμ. As Cμ increases to 0.0197 and 0.0338, the unsteady wake of the square cylinder is significantly attenuated and the process of flow separation is notably restrained. It is shown that distributed suction through side-walls effectively controls the unsteady shear-layer separation and wake flows of the square cylinder.