Hydrological series data are non-stationary and nonlinear. However, certain data-driven forecasting methods assume that streamflow series are stable, which contradicts reality and causes the simulated value to deviate from the observed one. Ensemble empirical mode decomposition (EEMD) was employed in this study to decompose runoff series into several stationary components and a trend. The long short-term memory (LSTM) model was used to build the prediction model for each sub-series. The model input set contained the historical flow series of the simulation station, its upstream hydrological station, and the historical meteorological element series. The final input of the LSTM model was selected by the MI method. To verify the effect of EEMD, this study used the Radial Basis Function (RBF) model to predict the sub-series, which was decomposed by EEMD. In addition, to study the simulation characteristics of the EEMD-LSTM model for different months of runoff, the GM(group by month)-EEMD-LSTM was set up for comparison. The key difference between the GM-EEMD-LSTM model and the EEMD-LSTM model is that the GM model must divide the runoff sequence on a monthly basis, followed by decomposition with EEMD and prediction with the LSTM model. The prediction results of the sub-series obtained by the LSTM and RBF exhibited better statistical performance than those of the original series, especially for the EEMD-LSTM. The overall GM-EEMD-LSTM model performance in low-water months was superior to that of the EEMD-LSTM model, but the simulation effect in the flood season was slightly lower than that of the EEMD-LSTM model. The simulation results of both models are significantly improved compared to those of the LSTM model.