The invention relates to a seawater desalting system in hydropower cogeneration and a method for desalting seawater, belonging to the field of seawater desalting. The seawater desalting system provided by the invention comprises a power station steam turbine, a heat pump and a seawater desalting unit, wherein the power station steam turbine is used for providing steam turbine exhaust and power steam for the heat pump; the heat pump is driven by the power steam to absorb the heat of the steam turbine exhaust and transfer the heat to material seawater; and the seawater desalting unit receives the material seawater preheated by the heat pump and carries out seawater desalting. According to the seawater desalting system and the method for desalting seawater in the invention, the heat of the steam turbine exhaust is absorbed to preheat the material seawater, so that the material seawater temperature is increased, the fresh water output is increased and the energy waste is reduced.