Analytical Hierarchy Process (AHP) is a system decision-making analysis approach which is utilized for the quantitative and qualitative analysis of the multi-objective and multi-criteria complex system problems. It is a powerful tool of the scientific decision-making for the complex systems. This article, firstly, determines the indicator system of the operation command management system and carries out the fuzzy comprehensive analysis and research of the application effectiveness of the operation command management system. It also evaluates the application effectiveness based on the method of AHP and the fuzzy comprehensive evaluation technique and finally builds an application effectiveness evaluation model. The numerical simulation results indicate that the judgment matrix of the application effectiveness evaluation model has satisfactory consistency, and the application effectiveness of the operation command management system is excellent, as well as the evaluation grade that is determined by the maximum membership principle is effective.