This paper proposes an effective method for suppressing the second harmonic dc bus voltage pulsation accounting for the second harmonic torque ripple in the permanent magnet synchronous generator (PMSG) system with asymmetric impedance. Neither the balanced current control nor the instantaneous power control can cope with the second harmonic dc bus voltage pulsation and the second harmonic torque ripple simultaneously in an asymmetric PMSG system. In this paper, the average power control is employed and only the positive sequence currents appear in the system, thus the second harmonic torque ripple will be avoided with balanced back electromagnetic forces. The second harmonic power and dc link voltage pulsations are then reduced by a compensation unit in parallel with dc bus diverting the second harmonic power. The effectiveness of the proposed method is verified through a small-scale wind turbine PMSG prototype with inherent asymmetry and deliberately introduced asymmetries.