Reducing the impact of artificial neural networks (ANN) affected by sources of uncertainty is crucial to improving the reliability of the flood prediction model. This study proposes an ensemble artificial neural network (EANN) model to predict the degree of flooding in coastal cities. Combined methods are used to reduce the model’s uncertainty, heuristic neural pathway strength feature selection is used to select inputs, the coupling method is used to optimize network architecture and parameters, and the integration method which paralleling three ANN models with different predicted lead periods ensemble together is used to capture output uncertainty. The EANN model has successfully predicted flooding in the Chinese coastal city of Macao during a typhoon, with convincing accuracy. The study also analyzed the impacts of both long and short training datasets with appropriate time intervals on ANN modeling performance. It was found that the performance of short training datasets, with appropriate time intervals, was similar to or better than models with long training datasets.