Command and control (C2) models of air defense weapon system such as target threat sequencing, weapon-target distribution and launch decision are lack of comprehensiveness, objectivity and flexibility currently. In order to solve the problems above, a novel command and control model decision method is proposed based on evaluation model. On the one hand, starting from three aspects including design goals, design principles and design methods independently, a design process of factor system which could sort out all influencing factors of the model hierarchically is established. On the other hand, based on the analysis of the characteristics of commonly used evaluation methods, a selection process for evaluation model which could choose appropriate evaluation model is proposed, aiming to realize the evaluation of factor system. In order to verify the performance of the proposed method, this paper uses this method to design a typical air defense weapon system target threat ranking model. The calculation results shown that the proposed method, which could provide a novel solution for the multi-factor decision process of the air defense weapon system, could be used in the design of the command and control model of the air defense weapon system.