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To overcome the limitations of the traditional stage-discharge models in describing the dynamic characteristics of a river, a machine leing method of non-parametric regression, the locally weighted regression method was used to estimate discharge. With the purpose of improving the precision and efficiency of river discharge estimation, a novel machine leing method is proposed:the clustering-tree weighted regression method. First, the training instances are clustered. Second, the k-nearest neighbor method is used to cluster new stage samples into the best-fit cluster. Finally, the daily discharge is estimated. In the estimation process, the interference of irrelevant information can be avoided, so that the precision and efficiency of daily discharge estimation are improved. Observed data from the Luding Hydrological Station were used for testing. The simulation results demonstrate that the precision of this method is high. This provides a new effective method for discharge estimation.