The invention discloses a small current grounding line selection device CT polarity error judgment method. The method comprises the following steps that when a grounding fault occurs, a fault branch zero sequence current is determined based on a fault line selected by a device; instantaneous values of all branch currents are recorded by the device sampling wave recording function; and all instantaneous values of all branch currents are calculated and compared, if prescriptive features are not met, branch CT polarity error exiting is determined, line selecting result is not reliable, and the condition is displayed on the device. Based on the premise that isolated neutral system small current grounding line selection device adopts zero sequence CT to obtain zero sequence currents of brancheson a bus, and with combination of the line selection results of the line selection device, the conclusion of whether zero sequence CT inverse connection in the branch existing is obtained through analysis and calculation of characteristics of each branch current when the single-phase grounding fault occurs in the branch.