In the permanent magnet wind power generation system, it is necessary to reduce the insulation damage of the stator winding caused by the pulse width modulation (PWM) high frequency pulse wave generated from the generator side converter, and reduce the generator loss caused by the harmonic current. Based on the analysis of the traditional PI control strategy, a new strategy is proposed, in which a resonant two-degree-of-freedom (R-2DOF) PID controller is designed by combining the resonant controller with a 2DOF PID controller, and particle swarm optimization (PSO) algorithm is used to optimize the controller parameters. The controller has strong current tracking capability, stable control and good harmonic current suppression. At the same time, the R_d damping type (filter capacitor branch series resistance) LCLLC filter is used for the generator side converter to attenuate the high-order harmonics in the PWM high frequency pulses. In comparison with the existing harmonics suppression strategy combining traditional PI control with R_d damping type LCL filter, the proposed controller can not only suppress current harmonics, but also achieve the no-error control of the current loop. Moreover, the proposed controller can reduce the influence of external disturbance and enhance the dynamic stability. Simulation experiment of permanent magnet synchronous generator is carried out on MATLAB/Simulink. Simulation results show that the LCLLC filter has a good effect on filtering the harmonic components of the PWM high frequency pulse wave. The R-2DOF PID controller can track the periodic signal without error and achieve the suppression of harmonics.