In order to solve the problem of the weapon system-of-systems of cost allocation problem of effective quantitative, In the process of weapon system-of-systems construction cost allocation method were studied. Based on the products of operational activity model, operational activity-to-system function mapping matrix, and system-to-system function mapping matrix in architecture products, operational activity-to-system mapping matrix of weapon system-of-systems is built. A method is put forward to compute the cost allocation of the weapon system-of-systems in the context of the importance of the operational activity is indiscrimination. The example results of the interceptive aerial defense weapon system-of-systems prove the feasibility and rationality of the method.