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The water quality prediction is an important basis to implement water pollution control programs. In this paper, the gray system method is used to build a mathematical model of water quality prediction for the Yangtze River and using computer to simulate it to complete the implementation of the method for solving the model. Finally we find the method to solve problem of predicting the water quality of Yangtze River. The key problems are focused on the following two issues. (1) If we do not take more effective control measures, we make prediction analysis of the future development trendbased on past data. (2). According to the prediction analysis, we use computer to simulate that how much sewage we need to address each year.