For the real engineering situation that the proportional-integral-derivative control law (PID) may not adapt to the non-minimum phase system property of hydro turbine set efficiently, a new non-minimum phase system control strategy of hydro turbine set is proposed. Firstly, a three order differential equations set of hydro turbine set is established according to the nonlinear hydro turbine model given by Institute of Electrical and Electronics Engineers (IEEE) assuming a non-elastic water column. Secondly, a control law of nonlinear non-minimum phase system is applied to regulate this system. It realizes the nonlinear control strategy of hydro turbine set and then it is compared with PID control law optimized by particle swarm optimization (PSO). The simulation results show that this non-minimum phase control strategy can be applied to the hydro turbine set effectively and the control effect is much more better than PID control law given that it can handle with the situation of huge speed disturbance, while PID control is invalid.