The frequency of global floods has increased, posing significant threats to economic development and human safety. Existing flood risk zoning studies in disaster prevention lack integration of the natural–economic–social chain and urban resilience factors. This study addresses this gap by constructing flood disaster risk and intensity indices using data from 31 provinces and 295 prefectural-level cities in China from 2011 to 2022. These indices incorporate natural (rainfall), economic (GDP), and social (population, built-up area) indicators to assess the flood likelihood and loss degree, providing comprehensive risk and intensity ratings. The study also examines the impact of resilience factors—environmental (green space), infrastructural (rainwater pipeline density), and natural resource (watershed areas)—on flood intensity. Findings reveal that high-risk regions are mainly in the Yangtze River Basin and southern regions, while high-intensity regions are primarily in the middle and lower Yangtze River and certain northwestern cities. Increasing rainwater pipeline density mitigates flood impacts in high-risk, high-intensity areas, while expanding green spaces and pipelines are effective in high-risk, low-intensity regions. This paper proposes a comprehensive flood hazard zoning mechanism integrating natural, economic, and social factors with urban resilience, offering insights and a scientific basis for urban flood management.