Accurate and consistent annual runoff prediction in regions is a hot topic in the management, optimization, and monitoring of water resources. A novel prediction model (ESMD-SE-WPD-LSTM) is presented in this study. Firstly, the extreme-point symmetric mode decomposition (ESMD) is used to produce several intrinsic mode functions (IMF) and a residual (Res) by decomposing the original runoff series.Secondly, the sample entropy (SE) method is employed to measure the complexity of each IMF. Thirdly, we adopt wavelet packet decomposition (WPD) to further decompose the IMF with the maximum SE into several appropriate components and detailed components. Then the LSTM model, a deep learning algorithm based recurrent approach, is employed to predict all components obtained in the previous step. Finally, the forecasting results of all components are aggregated to generate the final prediction.The proposed model, which is applied to five annual series from different areas in China, is evaluated based on four quantitative indexes (R, NSEC, MAPE and RMSE). The results indicate that the ESMD-SE-WPD-LSTM outperforms other benchmark models in terms of four quantitative indexes. Hence the proposed model can provide higher accuracy and consistency for annual runoff prediction, making it an efficient instrument for scientific management and planning of water resources.