In flexible grounding system under high-impedance grounding faults, harmonic injection from distributed generators (DG) can distort fault features, making accurate fault identification difficult. To address this issue, a high- impedance fault line selection method for flexible grounding systems that accounts for DG harmonic injection is proposed. First, a flexible grounding system model is established, and the impact of the transient control process caused by the withdrawal of the neutral-point small resistor on system parameters is analyzed. Then, based on the system parameter distribution characteristics after the small resistance is withdrawn, the dominant resonant components among feeder groups are extracted, and the phase difference characteristics between the dominant resonant components of faulty and healthy feeders are quantified. Finally, the cross-wavelet transform is applied to extract highly correlated time-domain features between lines, and stationarity tests are applied to eliminate the interference of DG-injected harmonics on the highly correlated time-domain signals. A phase difference coefficient fault selection criterion is constructed, enabling high-impedance fault line selection under coupled harmonic-transient scenarios. Simulink simulation results show that the proposed method is applicable to grounding faults with a transition resistance of up to 4000 Ω and maintains high reliability under extreme conditions such as arcing grounding and strong noise interference.