AbstractHarmonic resonance is caused by harmonic source matching resonance frequency and presents the characteristics of decentralization and whole network in modern grids. The current resonance suppression methods mainly focus on reducing the harmonic source, and are suitable for single‐site and small‐scale grids. This paper presents a new method for suppressing parallel resonance at system level. The holistic harmonic resonance is suppressed by reducing the harmonic impedance. In addition, new resonances are prevented by weakening the coupling between resonance and non‐resonance frequencies. The resonance modal analysis and resonance frequency shift (RFS) are employed to optimize harmonic impedance. Simulation results indicate that the capacitance parameter has higher sensitivity and is theoretically more suitable for RFS. Considering the accuracy of modal frequency sensitivity, a variable‐limit genetic algorithm for iteration is proposed. The validity of the proposed method was verified using an IEEE 14‐bus test network.