Aiming at the problem of ultra-low-frequency oscillation (ULFO) caused by an irrational setting of governor parameters of high-head hydraulic turbine units, this paper proposes a method to optimize the additional damping control parameters of the governor to suppress ULFO. Firstly, the mechanism of ULFO is elaborated and the effect of system damping torque on ULFO is analyzed. Secondly, Hamilton’s theory is used to rank the magnitude of each unit’s contribution to the ULFO. Then, the parameters of the damping controller are optimized using the variational modal decomposition–Hilbert transform method and the Grey Wolf Optimization algorithm. It realizes the phase compensation of the hydroelectric unit governor and suppresses the ultra-low-frequency oscillation. Finally, the proposed method is validated using the simulation conducted in CloudPSS. The test results indicate that the proposed method can effectively suppress the ULFO caused by the high-head hydroelectric unit.