The invention provides a zero-sequence current protection method and system, and the method comprises the steps: calculating zero-sequence currents of a first circuit and a second circuit of a commonbus of two ends in a common-tower three-loop circuit; building an actual model of the common-tower three-loop circuit based on an EMTP simulation model, and respectively calculating the zero-sequencecirculation coefficients of the first and second circuits; respectively calculating the zero-sequence currents of the first and second circuits after the zero-sequence circulation compensation based on the zero-sequence circulation coefficients of the first and second circuits; and judging whether to carry out the zero-sequence protection operation or not according to the zero-sequence currents ofthe first and second circuits and the zero-sequence currents of the first and second circuits after the zero-sequence circulation compensation. The method provided by the invention is accurate and effective, accords with the actual engineering, and effectively avoids the misoperation of the zero-sequence current protection of the circuit.