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In this paper, the entire process of the flow around a fixed square cylinder and the moving surface boundary-layer control (MSBC) at a low Reynolds number was numerically simulated. Two small rotating circular cylinders were located in each of the two rear corners of the square cylinder, respectively, to transfer momentum into the near wake behind the square cylinder. The rotations of the two circular cylinders were realized via dynamic mesh technology, when the two-dimensional incompressible Navier–Stokes equations for the flow around the square cylinder were solved. We analyzed the effects of different rotation directions, wind angles θ, and velocity ratios k (the ratio of the tangential velocity of the rotating cylinder to the incoming flow velocity) on the wake of flow around a square cylinder to evaluate the control effectiveness of the MSBC method. In the present work, the aerodynamic forces, the pressure distributions, and the wake patterns of the square cylinder are discussed in detail. The results show that the high suction areas near the surfaces of the rotating cylinders can delay or prevent the separation of the shear layer, reduce the wake width, achieve drag reduction, and eliminate the alternating vortex shedding. For a wind angle of 0°, the inward rotation of the small circular cylinders is the optimal arrangement to manipulate the wake vortex street behind the square cylinder, and k=2 is the optimal velocity ratio between the control effectiveness and external energy consumption.