With the global climate change and the rapid urbanization process, there is an increase in the risk of urban floods. Therefore, undertaking risk studies of urban floods, especially the depth prediction of urban flood is very important for urban flood control. In this study, an urban flood data warehouse was established with available structured and unstructured urban flood data. In this study, an urban flood data warehouse was established with available structured and unstructured urban flood data. Based on this, a regression model to predict the depth of urban flooded areas was constructed with deep learning algorithm, named Gradient Boosting Decision Tree (GBDT). The flood condition factors used in modeling were rainfall, rainfall duration, peak rainfall, evaporation, land use (the proportion of roads, woodlands, grasslands, water bodies and building), permeability, catchment area, and slope. Based on the rainfall data of different rainfall return periods, flood condition maps were produced using GIS. In addition, the feature importance of these conditioning factors was determined based on the regression model. The results demonstrated that the growth rate of the number and depth of the water accumulation points increased significantly after the rainfall return period of ‘once in every two years’ in Zhengzhou City, and the flooded areas mainly occurred in the old urban areas and parts of southern Zhengzhou. The relative error of prediction results was 11.52%, which verifies the applicability and validity of the method in the depth prediction of urban floods. The results of this study can provide a scientific basis for urban flood control and drainage. Display omitted •Data warehouse and deep learning algorithm were used to assess urban flood risk.•The GBDT model shows 88.48% accuracy in the depth of water accumulation prediction.•Flood risk analysis of Zhengzhou is mapping using the GBDT model.