A locking method and apparatus for preventing differential malfunction due to reverse polarity connection of balance winding CT is provided. The operation mode is collecting the current of each phaseof the series transformer balance winding, calculating the phase of the three-phase current in real time, comparing the phase of each phase current with the phase of the other phase current respectively, when the phase difference is greater than the closed lock value, the zero-sequence differential protection is blocked; When the ratio of differential current of zero sequence differential protection to differential current of longitudinal differential protection is larger than the closed lock value, zero sequence differential protection is locked. The invention can reliably reflect whether thepolarity of the balance winding CT is reversed or not, prevent the protection from maloperation, and can be widely applied to the zero-sequence differential protection of the series transformer.