This paper presents a detailed numerical investigation of the influence of re-organized shock waves on the flow separation for a highly-loaded transonic compressor cascade. The boundary layer suction (BLS) was used to control the location and strength of shock waves, with the aspirated slot locating at 49% chord, where is just downstream of the impingement point of shock wave at the leading edge. The numerical simulation is based on NUMECA, a commercial software, where the cell-centered control volume approach with third-order spatial accuracy is used to solve the 3-D Reynolds-averaged Navier-Stokes equations under the Cartesian coordinate system. Several conclusions can be made through the observation of the numerical results. (1) Multiple shock waves in cascade passage leaded the velocity deficits of boundary layer on suction surface downstream of shock wave, resulting in seriously separated flow on the suction side of blade, especially when the front shock wave is much stronger than the rest of the shocks. (2) BLS with small mass flow rate can not effectively improve the boundary layer. When the impingement point of oblique shock wave coming from cascade leading edge is bled to downstream of the passage shock wave by BLS, the boundary layer flow is greatly improved. However, if the BLS mass flow rate exceeds a critical value (1.2%), the boundary layer downstream of shock wave would separate from suction surface. (3) At the blade mid-span, the aerodynamic performance of compressor blade is improved as BLS mass flow rate increases. The optimum BLS is about 1.2%. Compared with the baseline case, the BLS with flow rate of 1.2% increases the total pressure recovery coefficient by 12%, and decreases diffusion factor by 18% and deviation angle to 7 ° while keeping the pressure rise constant. (4) The three dimensional flow structure of the compressor cascade ranged from 25% span to 75% span was improved greatly with the 1.2% BLS flow rate. However it could not control the development of the corner boundary layer effectively. This paper presents a detailed numerical investigation of the influence of re-organized shock waves on the flow separation for a highly-loaded transonic compressor cascade. The boundary layer suction (BLS) was used to control the location and strength of shock waves, with the aspirated slot locating at 49% chord, where is just just downstream of the impingement point of shock wave at the leading edge. The numerical simulation is based on NUMECA, a commercial software, where the cell-centered control volume approach with third-order spatial accuracy is used to solve the 3-D Reynolds-averaged Navier-Stokes equations under the observation of the numerical results. (1) Multiple shock waves in cascade passage leaded the velocity deficits of boundary layer on suction surface downstream of shock wave, resulting in seriously separated flow on the suction side of blade, especially when the front shock wave is much stronger than the rest of the shocks. (2) BLS with small mass flow rate can not effectively improve the boundary layer. When the impingement point of oblique shock wave coming from cascade leading edge is bled to downstream of the passage shock wave by BLS, the boundary However, if the BLS mass flow rate exceeds a critical value (1.2%), the boundary layer downstream of shock wave would separate from the suction surface. (3) At the blade mid-span, the aerodynamic performance of Compared with the baseline case, the BLS with flow rate of 1.2% increases the total pressure recovery coefficient by 12%, and reduces diffusion factor by 18% and the deviation angle to 7 ° while keeping the pressure rise constant. (4) The three dimensional flow structure of the compressor cascade ranged from 25% span to 75% span was improved greatly with the 1.2% BLS flow rate. However it could not control t he development of the corner boundary layer effectively.