The invention discloses a small-current single-phase grounding fault line selection method based on fast S transform. The small-current single-phase grounding fault line selection method comprises the steps of carrying out time-frequency analysis on transient zero-sequence currents of a faulty line and non-fault lines by utilizing fast S transform, calculating to obtain a one-dimensional mode coefficient and a one-dimensional phase angle value of each line after FST, calculating an energy value of each line, regarding the line with the maximum energy value as an alternative faulty line, regarding a non-alternative line as a phase angle reference comparison line, and taking whether an absolute value of a phase angle difference at a main frequency point in a transient feature frequency band after FST of the alternative faulty line and the phase angle reference comparison line is greater than a set threshold value as a line selection criterion. The small-current single-phase grounding fault line selection method avoids the influence of grid interference and accidental factors, makes full use of the transient signal time, amplitude, frequency and phase angle information, can select the faulty line quickly and accurately, is not affected by the neutral point grounding method, and has good adaptability.