The prediction of annual runoff in the Lower Yellow River can provide an important theoretical basis for effective reservoir management, flood control and disaster reduction, river and beach management, rational utilization of regional water and sediment resources. To solve this problem and improve the prediction accuracy, permutation entropy (PE) was used to extract the pseudo-components of modified ensemble empirical mode decomposition (MEEMD) to decompose time series to reduce the non-stationarity of time series. However, the pseudo-component was disordered and difficult to predict, therefore, the pseudo-component was decomposed by ensemble empirical mode decomposition (EEMD). Then, intrinsic mode functions (IMFs) and trend were predicted by autoregressive integrated moving average (ARIMA) which has strong ability of approximation to stationary series. A new coupling model based on MEEMD-ARIMA was constructed and applied to runoff prediction in the Lower Yellow River. The results showed that the model had higher accuracy and was superior to the CEEMD-ARIMA model or EEMD-ARIMA model. Therefore, it can provide a new idea and method for annual runoff prediction.