The existing flood regulation calculation methods for pumped storage power stations mostly neglect the hydraulic linkage between upper and lower reservoirs and tend to oversimplify scenarios involving the superposition of full-generation flow and natural floods. To address these issues, a flood regulation calculation method for the joint operation of upper and lower reservoirs in pumped storage power stations based on a segmented iterative method was proposed. This model established a mathematical framework that captured the complete water exchange and hydraulic coupling relationship between the upper and lower reservoirs and applied a segmented iterative algorithm to finely resolve the dynamic variations in water level and flow of the upper and lower reservoirs. On this basis, the model integrated a sliding combination approach to construct a flood encounter scenario matrix, simulating the impacts of various operating conditions and flood encounter scenarios on reservoir operations. A dynamic reserved reservoir capacity control strategy was proposed to ensure the safe operation of the power station and meet subsequent power generation needs. Case study results indicate that the proposed model can accurately and reliably simulate the dynamic response of upper and lower reservoirs under complex flood scenarios and effectively reveal the critical influences of flood encounter timing, operational status of the power station, and reserved reservoir capacity control strategies on hydrological conditions of the reservoirs. The most unfavorable flood encounter scenario identified by the model aligns with the operational characteristics of pumped storage power stations, offering a scientific reference for their engineering design and safe operation.