To solve the problem of transient method like wavelet difficult to determine the power frequency, this paper proposes a fault line selection method for neutral indirectly grounding system based on the waveform similarity of zero-sequence current. Based on the analysis of zero-sequence current for neutral indirectly grounding system, zero-sequence current waveform of non-fault lines are similar and very different from the fault line. This paper introduces mutual approximate entropy for fault line selection, by computing the mutual approximate entropy value of zero-sequence current sampling value between two outgoing lines with the same bus. Then the fault line is selected by judging the zero-sequence current waveform similarity of two lines. Simulation result shows the method shares the merit of being easy to implement, almost not effected by the high grounding resistance or power gird structure and fault initial condition, and accurate fault line selection.