The invention discloses a longitudinal differential protection zero suppression y-side compensation method for a transformer. The method is applicable to main transformers of various voltage levels of substations of various voltage levels of a power transmission and distribution network to complete current phase compensation of longitudinal differential protection phase current difference eliminating zero sequence current y-side phase shift for a YNy6 transformer. The method includes the steps of using Y-connection means for connecting TA secondary windings at the high-voltage side and low-voltage side of the YNy6 transformer, conducting phase shifting for Y side according to the formula described in the description, and conducting phase shifting for y side according to the formula described in the description.