Based on the structure of intelligence support system, establish the hierarchical structure evaluation index model for intelligence support system. According to the model, describe the application process of group hierarchy analytic algorithm in intelligence support system effectiveness evaluation. The simulation result shows that the algorithm can achieve the group weighting coefficient of every evaluation index under battle conditions. The method also can carry out effectiveness evaluation for intelligence support system. Meanwhile, it also provides a basis for optimum development and practical operation for the intelligence support system.