Aiming at the problem that the current passive line selection method has insufficient reliability in resonance and high resistance grounding faults, a fault line selection method for distribution network based on injected square wave signal and generalized S-transform energy entropy was proposed. Firstly, the distribution characteristics of the injected signal in the system when a single-phase ground fault occurs were analyzed, and the frequency selection of the injected square wave signal was reasonably analyzed on this basis. Secondly, wavelet threshold algorithm and fast independent component analysis were used to preprocess the zero-sequence current after the injection signal to achieve the effect of filtering noise and power frequency components. Finally, the generalized S-transform was applied to the preprocessed zero-sequence current signal to calculate the energy entropy of the generalized S-transform under the characteristic frequency of the injected signal, and the fault line was determined by comparing the entropy value. The simulation and on-site waveform verification results show that the proposed line selection method has strong applicability and reliability, can achieve accurate line selection under different working conditions, and has good anti-noise ability and high transition resistance ability.