Non-full-phase operation is a common asymmetric operational state in a power system. It will affect line zero-sequence current protection, causing it to lose selectivity and override. Therefore, the setting calculation principle of line zero-sequence current protection is studied. Then the calculation formulas of the zero-sequence branch coefficient under short-circuit fault and non-full-phase operation are deduced. By comparing the calculation formula of zero-sequence branch coefficient in two cases, the reason for the override of zero-sequence current protection under non-full-phase operation is analyzed. Compared with the zero-sequence branch coefficient of a short-circuit fault, the greater the zero-sequence branch coefficient of non-full-phase operation is, the easier the occurrence of override. Combined with the example of the IEEE39 bus system, it is verified that the increase of zero-sequence branch coefficient may cause the line zero-sequence current protection to override in the condition of non-full-phase operation. Finally, given the problem that zero-sequence current protection may override during non-full-phase operation, coping strategies are given from the two aspects of settings off-line verification and on-line management. This work is supported by the National Key Research and Development Program of China (No. 2016YFB0900100).