Abstract: This paper proposes a new comprehensive valuation method based on characteristic of information system and the property that wavelet can smooth data and adapt to the change of function. Furthermore, the dilation and shifts that are the parameters of wavelet function and the weight of neural network structure are calculated by conjugated gradient algorithm in term of the latest mean squared energy criterion.The results shown by the simulation that the method was effective and veracity for comprehensive evaluation of information system, and can provide a new way for evaluation research of information system.