For one type of civil helicopter, optimal design on aerodynamic performance of cooling hole intakes in the engine bay cooling system is studied. Two kinds of air collecting device are designed referring to applicant power unit (APU) intake system. The aerodynamic performance of the three cooling hole intakes in the condition of forward flight with various velocities and climb flight with different climbing rates are analyzed using numerical simulation method. The results show that the air collecting device designed according to scoop type has the best air collecting effect when the helicopter is flying forward at a high speed. Meanwhile, there is no improvement on aerodynamic performance of cooling hole intakes when helicopter is flying forward at a low speed. The air collecting device based on flush type also has a good function of improving air intake performance. And the most obvious advantage is to ensure a high cooling air flow in all flight conditions. Reasonably, it seems that the air collecting device designed based on flush type is more suitable for helicopter, which well points out the direction of the subsequent optimal design research.