Protection in flexible grounding systems mainly relies on time-limited zero-sequence overcurrent protection methods used in low-resistance grounding systems, which have limited capability to tolerate transition resistance. As a result, existing methods struggle to effectively detect faulty feeders. Aiming at this problem, a detection method based on the amplitude ratio and phase difference of zero-sequence currents is proposed. First, time-domain equations are used to analyze the zero-sequence currents between each feeder and the neutral point after low-resistance grounding. Then, by incorporating the inherent parameters of the distribution network, the specific differences between the amplitude ratio and phase difference of each feeder after adding the small resistors are obtained. Finally, by comparing the amplitude ratio of the zero-sequence current between the faulty feeder and the neutral point, it is found to be significantly higher than that of healthy feeders, thus forming Criterion 1. Additionally, by analyzing the phase difference of the zero-sequence current between the faulty feeder and the neutral point, it is found to differ by 90° from healthy feeders, thus forming Criterion 2. Simulation and field test results indicate that the proposed method can accurately detect single-phase high-impedance ground faults in flexible grounding systems, and is robust against current transformer polarity reversal, data loss, intermittent arcs, and strong noise.