In winter, the water transfer channel of the Middle Route of South-to-North Water Transfer Project (MR-StNWTP) in China always encounters ice problems. The preciously simulation and prediction of water temperature is essential for analyzing the ice condition, which is important for the safety control of the water transfer channel in winter. Due to the difference of specific heat between water and air, when the air temperature rises and falls dramatically, the range of change of water temperature is relatively small and has a lag, which often affects the accuracy of simulation and prediction of water temperature based on air temperature. In the present study, a new approach for simulating and predicting water temperature in water transfer channels in winter has been proposed. By coupling the neural network theory to equations describing water temperature, a model has been developed for predicting water temperature. The temperature data of prototype observations in winter are preprocessed through the wavelet decomposition and noise reduction. Then, the wavelet soft threshold denoising method is used to eliminate the fluctuation of certain temperature data of prototype observations, and the corresponding water temperature is calculated afterward. Compared to calculation results using both general neural network and multiple regression approaches, the calculation results using the proposed model agree well with those of prototype measurements and can effectively improve the accuracy of prediction of water temperature.