The invention provides a method for braking a magnetizing inrush current in the differential protection of an ultra-high voltage transformer, which comprises the following steps: acquiring a corresponding magnetizing inrush current criterion of each phase by the weight of an amplitude bias current, the weight of a secondary harmonic current and a symmetry degree of the waveform of each phase; and braking the magnetizing inrush currents of the phases whose magnetizing inrush current criterions are greater than a magnetizing inrush current braking coefficient. The method provided by the invention comprehensively considers the sizes of the three parameters, i.e. the weight of the amplitude bias current, the weight of the secondary harmonic current and the symmetry degree of the waveform. The increase or decrease of only one of the parameters cannot determine whether the whole magnetizing inrush current criterion is greater than or less than the magnetizing inrush current braking coefficient so as to solve the defect of only utilizing the secondary harmonic as the magnetizing inrush current criterion in the prior art. The invention makes the braking of the magnetizing inrush current more reliable so as to have a more accurate tripping of the differential protection of the transformer without causing false tripping or refuse operation. The invention also provides a system for braking the magnetizing inrush current in the differential protection of the ultra-high voltage transformer.