Nowadays, floods are occurring frequently around the world, and the Yangtze River Delta in China is one of the most vulnerable areas. This study used the Yangtze River Delta as the research object, established the flood disaster risk analysis model, calculated the indicator weights using the entropy weight method, and used three Multi-Criteria Decision-Making (MCDM) methods to compare and analyze the flood disaster risk in four administrative units of Yangtze River Delta (Shanghai City, Jiangsu Province, Zhejiang Province, and Anhui Province). Based on the weight estimation results, vegetation coverage was the priority in all evaluation criteria, followed by the proportion of the illiterate population aged 15 and over, drainage density, proportion of crop sown area, and building density. The ranking results show that the flood disaster risk is highest in Jiangsu, followed by Anhui. Shanghai and Zhejiang ranked third and fourth, respectively. Furthermore, a sensitivity analysis of the indicator weights was conducted considering that the ranking results mainly depend on the criteria weight. The results of the sensitivity analysis show that the main factors influencing the flood disaster risk level in the Yangtze River Delta are agricultural factors, followed by population density, drainage density, and the number of medical and health institutions. Also, in terms of meteorological and geographical conditions, exposure, vulnerability, and disaster loss, Jiangsu has the highest flood disaster risk, while Anhui has the highest flood disaster risk in terms of emergency and recovery capabilities. The findings can provide useful information on disaster prevention and mitigation managers.