In recent years, the phenomena of “seeing the sea in cities” and “seeing the river in cities” have occurred from time to time, which have aroused widespread concern among experts and scholars. In order to study the interaction between urbanization level and flood risk, we used ArcGIS technology and the comprehensive evaluation method to evaluate the flood risk in some administrative districts of Nanjing City at different urbanization levels, taking into account the factors of disaster-causing factors, disaster-breeding environment, disaster-bearing body and flood mitigation capacity. The results show that with the increase of urbanization level, the overall flood risk in the study area shows an increasing trend, and the flood risk of the districts is basically positively correlated with the urbanization level, among which Qinhuai and Gulou district are at the highest risk level, followed by Jianye and Yuhuatai district, whereas Jiangning and Lishui district have been maintaining a low risk level. The research results can correctly reflect the actual distribution of flood risk in Nanjing, indicating the validity of the research method and the reliability of the research results. Therefore, it can provide a theoretical support for flood risk management of relevant government departments.