To solve this problem that harmonic grounding system fault line zero sequence admittance levy does not highlight, this paper proposes a new resonant grounding line selection method based on EMD. In this method, each line zero sequence admittance is decomposed with EMD, characteristic component is extracted, and the fault line is selected by comparing the characteristic component symbols of the fault line and non-fault lines. Extensive simulations show that this method is not impacted by the ground fault resistance and the initial angle, and can accurately select the fault line.