In order to provide an effective method to control flight delay and study the influences of independent delay, an algorithm of independent delay and propagation delay is proposed.Based on the distribution of independent delays, a stochastic optimization model of aircraft routing is developed.During computation, the stochastic model is transformed into a deterministic model to reduce the difficulty in solving process.The model is verified by operation data from a large domestic airline company.The results indicate that this algorithm can reduce propagated delay by 28%, while the cost is reduced by 17.37%.It is shown that the stochastic optimization model based on delay analysis can improve the robustness of flight schedule.