Based on the flow field of a counter-rotating compressor, numerical investigation was conducted on the endwall boundary layer suction of both rotors in the stage environment. Research results show that as the suction flow rate increases, the compressor efficiency increases firstly and then decreases, and the efficiency of compressor improves by 1.03% for the best combined suction scheme. Suction can control the tip leakage flow effectively, and low-speed area near the pressure surface in the blade passage of both rotors almost disappears after suction, which increases tip region flow capacity greatly. On the other hand, suction also enlarge the flow separation range of the anti-clockwise rotating rotor (R2) suction surface trailing edge at the high blade span, resulting in larger flow loss. On the whole, suction improves the tip region flow field significantly. The stall of original compressor is induced by R2 tip leakage flow. As suction can effectively control R2 tip leakage flow, suction widens the stable working range of compressor and the surge margin improvement is 6.43% after suction. Meanwhile suction changes the flow instability mechanism and after suction the aerodynamic stall mainly results from large flow separation of blade suction surface.