Aiming at the problem of operational effectiveness evaluation of anti-UAV reconnaissance intelligence system, an operational effectiveness evaluation model is constructed. The operational mission and main functions of the reconnaissance and intelligence system are analyzed, and the effectiveness evaluation index system is constructed and optimized. The analytic hierarchy process (AHP) and fuzzy comprehensive evaluation method are used to evaluate the operational effectiveness of the reconnaissance and intelligence system, and the evaluation results are given. The results show that the method has clear logic, strong operability, and simple and clear calculation results, which is easy for decision makers to accept and understand.