Urban flooding disasters endanger people’s lives and property while causing significant economic damage to cities. To further improve the efficiency of urban flooding governance and promote the optimal allocation of resources, this article selects the number of people in flood control, medical and health security, financial expenditure on flood control, affected population, and direct economic loss as evaluation indicators from the input–output perspective; it measures the efficiency of urban flooding governance in 30 provincial capitals in China from 2012 to 2021 using the DEA model and Malmquist index method and identifies the key factors affecting the efficiency of urban flooding governance. The research results show that in 2021, the average value of the comprehensive technical efficiency of flood disaster governance in 30 provincial capitals in China was 0.408, the development trend was not optimistic, and the constraint factor was scale efficiency. The interannual average value of the total factor productivity index of urban flood disaster governance from 2012 to 2021 was 0.976, and the overall trend was decreasing year by year, during which some cities were able to achieve a yearly increase in governance efficiency, but most cities still faced a severe situation in flood disaster governance. The total factor productivity index varied enormously across towns with the variation in annual precipitation; the greater the annual precipitation, the greater the total factor productivity index of urban flooding disaster governance in the urban agglomerations, and the comprehensive technical efficiency change was consistent with its trend change. This consistency has a positive contribution to the total factor productivity index of urban flooding disaster governance.