To research the problem of flight delays occurring in rush hour of busy airport which make airport’s operation lower efficiency, the effect of congestion pricing being aimed at rush hour on slot demand is analyzed. A bi-level programming model of airport slot management for multi-user is established to determine the congestion pricing rate and corresponding flight flow, which considers the characteristic of direct flight and connecting flight. The case analysis shows that the volatility of flight volume and average delay time in different time are decreased. The model is an effective method of reducing flight delays and improving operation efficiency of busy airport.