In order to study the flight operations risk propagation mechanism, based on the civil aviation flight operation procedures, at first, the flight data and the working performances of airlines, airports, crew, aircraft and air traffic control were collected as research samples. Then, the experience network construction method and phasespace of time series reconstruction method and the Spearman correlation coefficient method were used to construct a complex network for flight operation risk propagation problems. After the calculation of the characteristic parameters, it was confirmed that the Spearman correlation coefficient method had built the network with best effect. After that, corresponding to the civil aviation common control methods, the concept of importance value r , improved infection rate β′ and improved recovery rate γ′ were introduced. An improved SIR model suitable for flight operation was proposed. Finally, the dynamic analysis of risk network propagation was carried out. The calculation results show that when the importance degree value equals 0.4, the peak value of the infection node density curve decreases by 10%, and the peak time is delayed by 5%. When the improved recovery rate is 0.9, the peak of the infected node is reduced by 6%. It is confirmed that adding the importance value and the improved recovery rate can effectively control risk networks spread. It shows that the identification and control to risk network key nodes, the improvement for the risk nodes recovery rate and speed, these can effectively improve the flight security.