The invention discloses a small current grounding system single-phase grounding fault wire selection method based on transient zero-module current. According to the method, a power network is subjected to three-phase modeling; different fault conditions are selected for performing single-phase grounding fault simulation experiment to obtain the transient zero-module current of each circuit; the data is extracted; the data is subjected to EMD (empirical mode decomposition); the time-domain energy of a plurality of IMFs (intrinsic mode functions) and the rest component are resolved; the energy of the IMFs and the energy of the rest components are added to obtain the energy sum of one circuit; the steps are repeated to obtain the energy sum of all circuits; the energy weighting coefficient of each circuit is calculated; the energy weighting coefficient of each circuit is compared; the circuit corresponding to the maximum energy weighting coefficient is a fault circuit. The peak value and the polarity of a first zero-module current pulse and the first instantaneous power peak polarity are compared; the zero-module current amplitude of the fault circuit is greater than the amplitude of a non-fault circuit, and the polarities are opposite. The method has the advantages that the influence of arc suppression coils and fault conditions is avoided; the fault circuit can be accurately selected.