To overcome the difficulty that existing hydrological models cannot accurately simulate hydrological processes with limited information in irrigated paddy areas in southern China, this paper presents a prediction model combining the Ensemble Empirical Mode Decomposition (EEMD) method and the Long Short-Term Memory (LSTM) network. Meteorological factors were set as the multivariate input to the model. Rainfall, regarded as the main variable affecting runoff, was decomposed and reconstructed into a combination of new series with stronger regularity by using the EEMD and K-means algorithm. The LSTM was used to explore the data laws and then to simulate and predict the runoff of the irrigated paddy areas. The Yangshudang (YSD) watershed of the Zhanghe Irrigation System (ZIS) in Hubei Province, China was taken as the study area. Compared with the other models, the results show that the EEMD-LSTM multivariate model had better simulation performance, with an NSE above 0.85. Among them, the R2, NSE, RMSE and RAE of the EEMD-LSTM(3) model were the best, and they were 0.85, 0.86, 1.106 and 0.35, respectively. The prediction accuracy of peak flows was better than other models, as well as the performance of runoff prediction in rainfall and nonrainfall events, while improving the NSE by 0.05, 0.24 and 0.24, respectively, compared with the EEMD-LSTM(1) model. Overall, the EEMD-LSTM multivariations model is suited for simulating and predicting the daily-scale rainfall–runoff process of irrigated paddy areas in southern China. It can provide technical support and help decision making for efficient utilization and management of water resources.