In order to solve the difficulty of single-phase high-resistance grounding fault detection in a low-resistance grounding system and the problem of protection rejection when single-phase grounding fault occurs under two feeders, a centralized protection scheme for such a system is proposed based on the comparisons of zero-sequence current amplitudes of the neutral line and each feeder. Combined with phasor analysis, the equivalent zero sequence networks of the system are established for when single-phase grounding faults under a single feeder or two feeders occur. Then the general characteristics under the two fault conditions are analyzed considering the different fault location, transition resistance and line capacitance to ground. The common fault characteristics are extracted to form the grounding protection criterion. This is applicable to single-phase grounding faults under single feeder or two feeders. The faults are isolated accurately. This method can clearly distinguish the single-phase grounding fault of the feeder and the bus side based on the relative difference of the zero-sequence current amplitudes of the neutral line and each feeder. The method remains valid even when the transition resistance is as high as 1 500 Ω. The protection algorithm has the advantages of low starting value, high sensitivity, large margin of setting value and good stability. It is suitable for the flexible operation of a distribution network. The simulation results show that the analysis of grounding fault characteristics is correct and the protection scheme is effective. This work is supported by the Key Project of National High-tech R & D Program of China (863 Program) (No. 2012AA050213) and the Science and Technology Project of China Southern Power Grid Company Limited (No. 030600KK 52200019[GDKJXM20200486]).