In order to effectively cope with the over-standard floods from the Taihu Basin and to coordinate the basin flooding and regional flood control safety, a hydrological and hydrodynamic mathematical model for the refined river network pump gate scheduling in the mainland region of Shanghai was constructed. Through multi-scenario numerical simulations of rainstorm and flood events, an optimal flood scheduling strategy was proposed using the entropy-weighted TOPSIS evaluation method to ensure flood safety in megacities. The results indicate that when over-standard floods in the Taihu Basin coincide with heavy or moderate rainfall events in Shanghai, a conditionally feasible basin diversion strategy can be implemented to achieve the optimal coordinated dispatching goal for both flood control and urban drainage.