Climate change, population increase, and urban expansion have increased the risk of flooding. Therefore, accurately identifying future changing patterns in the flood risk is essential. For this purpose, this study elaborated a new framework for a basin scale that employs a future land-use simulation model, a factor spatialization technique, and a novel hybrid model for scenario-based flood risk assessment in 2030 and 2050. Three land-use scenarios (i.e., natural growth scenario, cropland protection scenario, and ecological protection scenario) were set and applied in Jinjiang Basin to explore the changes in future flood risk under these scenarios. The results indicate the different degrees of increase in flood risk that will occur in the three scenarios. Under the natural growth (NG) scenario, the city will expand rapidly with the growth of population and economy, and the total area with high and very high flood risk will increase by 371.30 km2 by 2050, as compared to 2020. However, under the ecological protection (EP) scenario, woodlands will be protected, and the growth in population, economy, and built-up lands will slow down with slightly increased risk of flooding. In this scenario, the total area with high and very high flood risk will increase by 113.75 km2 by 2050. Under the cropland protection (CP) scenario, the loss of croplands will have been effectively stopped, and the flood risk will not show a significant increase under this scenario, with an increase by only 90.96 km2 by 2050, similar to the EP scenario. Spatially, these increased flood risks mainly locate at the periphery of existing built-up lands, and the high-flood-risk zones are mainly distributed in the southeast of the Jinjiang Basin. The information about increasing flood risk determined by the framework provides insight into the spatio-temporal characteristics of future flood-prone areas, which facilitates reasonable flood mitigation measures to be developed at the most critical locations in the region.