Counter-drone operation is an important part of air and missile operations. In view of the problems that the counter-drone operation capability is subject to the effect of joint air and missile defense system, and the evaluation capability is difficult to perform comprehensively with the counter-drone operation being divorced from the joint air and missile defense system, an evaluation index system of the joint air and missile defense and drone operation capability is constructed, and an evaluation model of the counter-drone operation capability is proposed under condition of joint air and missile defense system. The game theory is utilized for synthesizing the subjective and objective weights of AHP-entropy weight method, and optimizing the weights of evaluation indicators. The results show that the method is reasonable and scientific through the verified examples, providing a theoretical basis for evaluating the anti-drone combat capability of the joint air defense and missile defense system.