As climate change becomes increasingly widespread, rapid, and intense, the frequency of heavy rainfall and floods continues to increase. This article establishes a prediction system using feature sets with multiple data dimensions, including meteorological data and socio-economic data. Based on data of historical floods in 31 provinces and municipalities in China from 2006 to 2018, five machine learning methods are compared to predict the direct economic losses. Among them, GBR performs the best with a goodness-of-fit of 90%. Combined with the input-output (IO) model, the indirect economic losses of agriculture to other sectors are calculated, and the total economic losses caused by floods can be predicted effectively by using the GBR-IO model. The model has a strong generalization ability with a minimum requirement of 80 pieces of data. The results of the data show that in China, provinces heavily reliant on agriculture suffered the most with the proportion of direct economic losses to provincial GDP exceeding 1‰. Therefore, some policy implications are provided to assist the government to take timely pre-disaster preventive measures and conduct post-disaster risk management, thereby reducing the economic losses caused by floods. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.