The third plenary session of the 20th CPC Central Committee stressed the need to improve disaster prevention, mitigation and relief capabilities, and promote the modernization of the national security system and capabilities. Based on the perspective of “disaster prevention responsibility”, this paper constructs a theoretical model of the impact of flood disasters on economic growth, and empirically investigates the dynamic impact and mechanism of natural disasters on urban economic growth by using the panel data of urban economy and the daily data of meteorological stations in China from 2000 to 2020. The results show that the intensity of flood disaster has a nonlinear impact on the economic growth of the city in the current year, and the stronger the urban flood control measures, the stronger the resilience of economic development. The results show that local governments can effectively carry out natural disaster prevention and management while pursuing economic growth goals.