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Rapid urbanization and exacerbated natural hazards, for example, floods, have been the big challenges for the sustainable development of many countries. Understanding the coupling coordination between urbanization and flood is important for promoting the sustainable development. However, there are few quantitative studies on the interaction between these two in China which is experiencing accelerated urbanization and climate change. In this paper, we developed an improved coupling coordination degree (CCD) model, applied Moran's I and projection pursuit model based on genetic algorithm to analyze the spatiotemporal distribution and spatial clustering effects of coupling coordination in urbanization–flood disasters system under the context of China's Five-Year Plan for National Economic and Social Development. Our results showed an upward trend of the comprehensive level of urbanization subsystem and a decreasing first and rising later trend of flood disaster subsystem in China from 2001 to 2018. There was a U-shaped relationship between the two subsystems during the research period. From 2001 to 2018, provinces with the moderate and slight uncoordinated development decreased by 9.68% and 16.13%, respectively, while provinces with the barely coordinated development increased by 16.21%. Spatially, there was a remarkable spatial dependency on CCD. The CCD between two subsystems in Northwestern China was higher than that in Southeastern China. Due to the effects of geographic position, rainfall, human activities, and economic development, the low-low (L-L) clusters concentrated in Southeastern China, and the high-high (H–H) clusters appeared in Northwestern China. Our results show that the improved CCD model, along with Moran's I analysis, can provide theoretical basis for policy makers to formulate reasonable measures for promoting the coupling coordination between urbanization and flood disasters. • Spatiotemporal distribution and dynamic evolution of nexus between urbanization and flood disasters were investigated. • Improved CCD model, Moran's I and projection pursuit model based on genetic algorithm were developed. • There was a U-shaped relationship in comprehensive level between urbanization and flood disasters. • CCD between two subsystems in Northwestern China was higher than that in Southeastern China. • There was a remarkable spatial clustering effects in CCD. [ABSTRACT FROM AUTHOR]