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In this paper, a mid-to long-term runoff forecast model is developed using an ideal point fuzzy neural network-Markov (NFNN-MKV) hybrid algorithm to improve the forecasting precision. Combining the advantages of the new fuzzy neural network and Markov prediction model, this model can solve the problem of stationary or volatile strong random process. Error statistics algorithms defined are used to evaluate the performance of models. A runoff prediction of Si Quan Reservoir is made by utilizing the modeling method and the history runoff data, with a comprehensive consideration of various runoff-impacting factors such as rainfall. Compared with the traditional fuzzy neural networks and Markov prediction models, the results show that NFNN-MKV hybrid algorithm has a good performance in faster convergence, better forecasting accuracy and significant improvement of neural network generalization.The absolute percentage error of the NFNN-MKV hybrid algorithm is less than 7.0%, MSE is less than 3.9, and qualification rate reaches 100%. For further comparison of the proposed model, NFNN-MKV model is employed to estimate (training and testing for 120-month-ahead prediction) and predict river discharge 156 months in Weijiabao of the Weihe River in China. The comparison among the results of NFNN-MKV model, the WNN model and the SVR model indicates that the NFNN-MKV model is able to significantly increase the prediction accuracy.