The invention discloses a differential protection method of a multi-tap special transformer. The differential protection method of the multi-tap special transformer is characterized by comprising the following steps that firstly, transformer differential protection constant-value calculation is performed based on per-unit values; secondly, multi-tap gear information of the multi-tap special transformer is obtained and verified; thirdly, current information of all sides of the transformer is obtained, and the per-unit values of the currents of all sides are calculated according to nameplate parameters of the transformer; fourthly, protection action conditions are calculated and judged by utilizing the currents of the per-unit values. The differential protection method of the multi-tap special transformer is suitable for special transformers with multiple taps performing on-load voltage regulation, and according to the structural characteristics of the multi-tap special transformer, the differential protection algorithm of the transformer based on the per-unit values is derived. Protection constant-value calculation is performed according to the per-unit values of current data with the per-unit value differential protection algorithm of the transformer. In practical application, a multi-tap gear information processing method is adopted, the gear information of the transformer and the current information of primary and secondary sides of the transformer are synthesized, and information of an action equation, a brake equation and the like of the differential protection values is calculated.