Abstract: Based on large eddy simulation method, combined with high order WENO/TCD hybrid scheme, flow separation control by micro-ramp and micro-vanes was simulated under the condition of Ma=2.5. The simulated results of the boundary layer thickness, the size and structure of the separation zone reveal that the micro vortex generators suppress the boundary layer separation. For the micro-ramp vortex generator, the incident shock compresses the wake of micro-ramp, which enhances the strength of streamwise vortex and makes the energy change between the boundary layer and out flow. The control mechanism of the micro-vanes is similar with micro-ramp, but the vortex pair can break easily in the downstream, which may affect the energy change between the boundary layer and out flow.