The invention discloses a water turbine speed regulator PID parameter optimizing method and system. The method comprises the steps that the speed regulator PID parameter optimizing overall objective function J restraining ultra-low frequency oscillation is obtained, optimization is conducted through the optimization algorithm, the optimal PID parameter is sought, and the overall objective function is minimal. According to the method, the value obtained after weighting of the frequency step response deviation absolute value integral and speed regulating system damping at the focused ultra-low frequency band integral serves as the optimization objective, the obtained speed regulator parameter integrates the speed regulator adjusting performance and damping level at the same time, accordingly, the problem of ultra-low frequency oscillation caused by speed regulator negative damping is solved, and the speed regulator adjusting dynamic quality is combined.