The invention discloses a differential protection method of a transformer. The differential protection method comprises the following steps: acquiring a three-phase action, a brake current, a zero-sequence action and a brake current of the transformer in a steady state; for each of the four acquired current samples, calculating a wavelet coefficient of each sample point in the current sample, calculating wavelet coefficient energy corresponding to each sample point, and further determining an energy threshold for the current sample; for any detection moment, determining the wavelet coefficientenergy corresponding to the three-phase action current, the three-phase brake current, the zero-sequence action current and the zero-sequence brake current of the transformer at the moment, and obtaining a detection result at the moment in combination with four predetermined energy thresholds so as to realize protection of the transformer. By applying the scheme of the invention, the fault condition can be quickly determined, so that fault protection can be carried out in time. The invention further discloses a differential protection system and device of the transformer and a storage medium,and the differential protection system and device have corresponding effects.