Pumped storage power station is an important regulating tool for peak load regulation and frequency regulation of the power grid, especially its primary frequency regulation function, which is of profound significance for the safety and stability of the power grid. As the core equipment of the pumped storage power station, the reversible design of the pump turbine makes it easy to have hydraulic fluctuation and mechanical instability when the unit runs to the “S” characteristic area, which will cause the frequency oscillation of the generator under the condition of primary frequency regulation. Therefore, some innovative work is studied in this paper: (1) an accurate hydraulic-mechanical-electrical coupling system mathematical model of pumped storage unit regulation system (PSURS) is established based on full characteristic curve of the pump turbine and seventh-order synchronous generator and excitation system; (2) the dynamic response characteristics of primary frequency regulation of pumped storage unit (PSU) under different water heads and different frequency disturbances are analyzed by numerical simulation; (3) in view of the unstable condition of the unit under the large frequency disturbance when it operates in the low head and small load area, the objective optimization function considering the ITAE index of hydraulic, mechanical, and electrical factors is proposed; and (4) fractional-order PID controller and the bacterial-foraging chemotaxis gravitational search algorithm (BCGSA) combined optimization strategy is used for PSURS optimization regulation and parameter optimization. The results show that the joint optimization strategy proposed in this paper has smaller objective function value, and makes the PSURS pass through the unbalanced area quickly, with better primary frequency regulation speed and smaller regulation depth.