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In a neutral non-effectively grounded power system, the correct identification and isolation of the faulty feeder on the occurrence of a single-phase earth fault is always a difficult task. To improve the level of distribution automation, a novel method of negative-sequence current compensation based adaptive zero-sequence over-voltage protection is put forward in this paper. On the basis of the analysis of the transient negative-sequence current, it can be proved that the negative sequence current through the faulty feeder is far higher than those through the sound feeder in any configuration of distribution network and neutral compensation modes. Therefore, an adaptive inverse time delay characteristic is adopted by the basic zero-sequence over-voltage protection. A compensated voltage is generated by means of multiplying the modal maximum of the negative-sequence current of the feeder by a settable compensated reactance, and then it is combined with the magnitude of the zero-sequence voltage to consist of the compounded compensated voltage. This compensated voltage is utilized to revise the characteristic of the inverse time-delay. By this means, the zero-sequence over-voltage protection will possess the selectivity adaptively. The effectiveness of the proposed method has been verified with the results of the theoretical analysis and simulations.