Frequently occurring flood disasters caused by extreme climate and urbanization processes have become the most common natural hazard and pose a great threat to human society. Therefore, urban flood risk assessment is of great significance for disaster mitigation and prevention. In this paper, the analytic hierarchy process (AHP) was applied to quantify the spatiotemporal variations in flood risk in Wuhan during 2000–2018. A comprehensive flood risk assessment index system was constructed from the hazard, sensitivity, and vulnerability components with seven indices. The results showed that the central urban area, especially the area in the west bank of the Yangtze river, had high risk due to its high flood sensitivity that was determined by land use type and high vulnerability with dense population and per unit GDP. Specifically, the Jianghan, Qiaokou, Jiangan, and Wuchang districts had the highest flood risk, more than 60% of whose area was in medium or above-medium risk regions. During 2000–2018, the flood risk overall showed an increasing trend, with Hongshan district increasing the most, and the year of 2010 was identified as a turning point for rapid risk increase. In addition, the comparison between the risk maps and actual historical inundation point records showed good agreement, indicating that the assessment framework and method proposed in this study can be useful to assist flood mitigation and management, and relevant policy recommendations were proposed based on the assessment results.