The safety risk situation of the air traffic management system will directly affect the safe operation of air transportation. Comprehensively considering the safety operation characteristics of air traffic management system, the evaluation index system of safety risk is constructed. The combination weights of the evaluation index are obtained by means of the Euclidean distance function. The matter-element analysis method is introduced to establish the matter-element model for safety risk assessment of air traffic management system. The empirical analysis shows that the matter-element analysis method can obtain the overall safety risk status of the air traffic management system, and at the same time can obtain the safety risk status of each evaluation index. This is helpful to take effective measures to improve the safety risk management level of the air traffic management department.