Flexible grounding systems combine the advantages of resonant grounding and low-resistance grounding systems. However, when using zero-sequence overcurrent protection, they exhibit poor tolerance to transition resistance. To address this issue, a fault line selection method is proposed to comprehensively utilize transient information in the low-resistance input stage and arcing coil compensation stage in flexible grounding systems. First, the zero-sequence transient currents of each line during the arc suppression coil compensation stage and the low-resistance input stage are analyzed. It is found that, during the arc suppression coil compensation stage, the faulted line has an additional current component passing through the transitional resistance compared to the healthy lines, while the expressions of transient zero-sequence currents of each line are the same during the low-resistance input stage. Next, by calculating the line-to-ground capacitance ratio based on the transient zero-sequence currents during the low-resistance input stage, the difference between the transient zero-sequence currents of each line during the arc suppression coil compensation stage is obtained using this ratio. The difference of transient zero-sequence currents between the faulted and healthy lines is the current passing through the transitional resistance, while that among the healthy lines is zero. Furthermore, by constructing a matrix of zero-sequence current difference, the fault selection is achieved by comparing the elements of each row and column of the matrix. Finally, the correctness and effectiveness of the proposed method are validated in PSCAD/EMTDC and a low-voltage experimental platform.