Floods have become increasingly frequent and pose more significant risks in delta plains due to rapid urbanization. While previous studies have primarily focused on urban flood management, there has been a limited exploration of coordinated flood control strategies that encompass cities, regions, and basins holistically. In response to this gap, our research aims to quantitatively assess flood control coordination under various scheduling rules and propose optimized strategies to enhance this coordination. Using the Wu-Cheng-Xi-Yu region as our case study, we observed that flood characteristics under different flood control coordination schemes varied slightly, especially the FI. Moreover, the effectiveness of different scheduling optimization schemes varied across different levels. Specifically, at the basin–region, basin–city, and region–city levels, Schemes S8, S7, and S5 demonstrated the highest coordination coefficients, with values of 0.80, 0.67, and 0.68, respectively. In comparison to the current scheduling Scheme (S0), these schemes resulted in significant improvements in flood coordination, with enhancements of 0.68, 0.37, and 0.22, respectively. Furthermore, our findings indicate that the most effective approach to strengthening flood control coordination involves implementing scheduling measures that reduce urban drainage while simultaneously improving the discharge capacity of the basin. Our results could help to alleviate the contradictions of flood control at different levels and provide a solid guarantee for water security.