In order to solve the problem of the poor effect using simply zero-sequence current to select fault line, the paper introduces a new method to select fault line for neutral indirect grounding system by transient main frequency components of zero-sequence current. Based on the feature analysis of zero-sequence current, the paper utilizes Prony algorithm to extract the main frequency components of transient information of each line. Because its transient main frequency waveforms are similar between the non-fault lines when the fault occurred in system, and there is a clear distinction between the fault line and non-fault line, so the integrated correlation coefficients are obtained to achieve the fault line selection correctly by correlation analysis. Theoretical analysis and simulation results show the new method has validity, strong anti-interference, and without setting. It can select fault line successfully with different conditions, including different transition resistance, different initial fault angel, different fault position and grounding modes, and further improve the protection margin.