The management of urban flood disasters is a systematic engineering project that requires a great amount of manpower, material resources, and financial resources, and the interaction and coordination degrees of various elements in the system deeply affect the efficiency of the final governance. According to the theories of synergy, composite systems, and sustainable development, this research first established an evaluation index system to determine the synergy degree of urban flood disaster emergency management from the four dimensions of prevention and preparation, monitoring and early warning, response and rescue, and recovery and reconstruction. Then, the synergy degree was explored by using the developed composite system synergy degree model on the basis of the panel data of 18 prefecture-level cities in Henan Province from 2013 to 2021, and synergy level change characteristics were analyzed from the perspectives of time and space. Finally, the obstacle degree model was applied to explore the obstacle factors affecting synergy degree development. The results showed that the overall level of the urban flood disaster emergency management coordination degree in Henan Province was relatively low, and there were significant differences in synergy among cities. Among them, 12 cities presented mild synergy, and 6 cities showed mild nonsynergy. The spatial correlation of the synergy degree was not stable, which revealed a lack of mature coordination mechanisms for flood disaster emergency management among cities. The analysis of obstacle factors showed that recovery and reconstruction subsystems were the main obstacle systems that affected the synergy degree.