In order to investigate the potential causative factors and mechanisms of accidents in the flight transit security system, and to further ensure the safety of civil aviation operation, based on the system theory and the gray correlation theory, and combining with the actual situation of the flight transit security operation process, the safety problems in the system were transformed into the control and feedback problems, and the safety control and feedback structure was mapped out. Using complex network theory to transform accident causation and its logical relationship, a directed weighted accident causation network model was constructed, the overall characteristics of the network and the connection of each node from different perspectives were quantitatively analyzed, such as the node degree, the network diameter and the average path length, etc., and then 16 important accident causation factors affecting the flight transit security system were selected. Through grey correlation analysis, the influence degree of each cause factor on the accident was judged, and the key cause factors that need to be prevented and controlled were finally determined. The results show that the personnel factor dominates the accidents in the flight crossing security system, and its sub-factors, such as speeding, insufficient number of personnel, error of towing personnel and illegal entry of personnel into the control area, are the key causal factors leading to the accidents.