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According to the Characteristics of complex object system, a comprehensive evaluation model for complex object system is established based on fuzzy theory and artificial neural network. To realize the intelligence and the visualization of the evaluation process, an intelligent comprehensive evaluation software system with the help of Visual Basic, database technique and MATLAB toolbox is designed. In addition, the key technologies in designing the evaluation system are discussed. It presents an effective and reasonable intelligent decision-making method for the comprehensive evaluation of complex object system.