Compared with conventional transformers, the rectiformer is special in connection mode, which is multi-tap and not equipped with the differential protection. In this paper, the differential protection algorithm for Multi-tap special transformer was derived. The regulating methods for the rectiformer were studied first, and then the rectiformer model of one electrolytic aluminium plant was built by PSCAD/EMTDC, characteristics of the rectiformer bank were also analyzed. The algorithm was derived on the basis of the per-unit system, and the processing methods of the regulating transformer’s tap position information were proposed. Finally, a contrast of differential protection algorithm between the multi-tap special transformer and the conventional transformer was made.