In order to analyze and study the flight operations risk propagation, and then effectively control flight safety, based on the complex network theory, a total of 29 terminal factors including crew, aircraft, and operating environment were selected as network nodes according to the Civil Aviation Administration's advisory notice firstly. Civil aviation safety monitoring records were counted, and an undirected network was constructed based on the node relationships. The relationships and occurrence probability between the nodes were counted, and a directed and weighted network was constructed. The concepts of improved infection rate and improved recovery rate were introduced, an improved SIR model suitable for flight operation risks was proposed. Finally, the initial infection range was clearly defined, and a multi-parameter control method was adopted. For directed and undirected networks, large-scale propagation and control simulations were calculated. The results indicate that the average shortest path of the directed network was 1.788, which belonged to the small-world network. The directed network infection node decreased 13.7% with the conventional control measures, higher than that of the undirected network. After 3 nodes control, the infected nodes peak drop rate was as high as 50.6%. The results confirm that nodes controlling based on the entry degree value is the most effective to suppress risk propagation in the directed and weighted network.