In this paper, the flow control system consists of some small microflaps located between the rear fins of the projectile. These microflaps can alter the flow field in the finned region of the projectile resulting in asymmetric pressure distribution and thus producing control forces and moments, furthermore to provide directional control for a supersonic projectile. Due to the small size and high speed characteristics of projectile, which is with fast and valid response characteristics, this flow control system has initially shown excellent potential in terms of supersonic flow control. The CFD simulation used here solves steady-state Reynolds-averaged Navier-Stokes equation with two-equation turbulence model k-ε. Firstly, we investigate the flow mechanism around microflap in supersonic flow, the flow fields around the microflap are complex, involving three-dimensional shock-shock, shock-boundary layer interactions. Secondly, for the microflap and the fin of Basic Finner configuration, the influence of microflap geometric parameters, microflap locations on aerodynamics is obtained and the interference mechanism is explored. Finally, several typical roll and pitch control layouts are described. According to the simulation results and their analysis, some preliminary conclusions can be drawn: by analyzing the flow interference mechanism between microflap and the fin, we find that the separated shocks ahead of the microflap, the bow shocks around microflap, and the trailing-edge wake, have influences on fin's surface pressure; among these factors, the bow shocks are stronger than separated shocks, furthermore it can generate larger high pressure region. Then we find out the aerodynamic characteristics of several typical control layouts at a supersonic speed, Ma=2.5, furthermore, hence nearly 4.8% drag is increase compared with the condition without microflap. As the number of microflaps increasing, the control aerodynamic forces and moments increases almost linearly. With a proper layout of the microflap's location, quick change in the surface pressure distribution can be achieved for rear fins of the projectile, the microflap should be mounted that can increase the high pressure zone, meanwhile, reduce the low pressure zone on the surface of fins, thus modulating the projectile's attitude can be realized.