As an area frequently suffering from storm surge, the Yangtze River Estuary in the East China Sea requires fast and accurate prediction of water level for disaster prevention and mitigation. Due to storm surge process being affected by the long-term and short-term correlation of multiple factors, this study attempts to introduce a data-driven idea into the water level prediction during storm surge. By collecting the observed meteorological data and water level data of 12 typhoons from 1986 to 2016 at the Lusi tidal station of Jiangsu Province, China near the north branch of the Yangtze River Estuary, a Long Short-Term Memory (LSTM) neural network model was constructed by using multi-factor time series to predict the water level during the storm surge period. This study concludes that the LSTM model performs precisely for 1 h prediction of water level during the storm surge period and it can provide a 15 h prediction of water level within a limited error, and the prediction performance of the LSTM model is visibly superior to the four traditional ML models by 41% in terms of Accuracy Coefficient.