The invention discloses a phase compensation method for eliminating zero sequence current employing a phase current difference of a YNy12 transformer. The phase compensation method is applied to main transformers with various voltage grades of substations with various voltage grades in a transmission and distribution network, and current phase compensation for eliminating the zero sequence current employing a longitudinal differential protection phase current difference of the YNy12 transformer is completed. The compensation method comprises the steps as follows: a star connection method is adopted by secondary windings of TAs at a high-voltage side and a low-voltage side of the YNy12 transformer; and current phase compensation is carried out on a differential protection Y side and a differential protection y side of the YNy12 transformer by adopting a calculation method for eliminating the zero sequence current employing the phase current difference, so that an external fault and a misoperation of the transformer caused by the zero sequence current are prevented. A current phase compensation method is carried out on the differential protection Y side of the YNy12 transformer by adopting the calculation method for eliminating the zero sequence current employing a sequential phase current difference on the basis of A-phase current; and the current phase compensation method is carried out on the y side of the YNy12 transformer by adopting the calculation method for eliminating the zero sequence current employing the sequential phase current difference and an in-phase current principle of the Y side and the y side.