The characteristics of excitation inrush current and its zero sequence component of high voltage built in transformer are studied and analyzed in this paper. Compared with the conventional transformer, the high-voltage built-in transformer inrush current zero sequence component is larger and decays more slowly under its structural characteristics, because the zero sequence current protection are more prone to misoperation. Based on EMTDC/PSCAD, the effect of residual magnetism, closing angle and operation mode on the zero sequence component of no-load transformer is analyzed. Besides, the misoperation probability of zero sequence current protection is given. It is recommended to ensure the normal operation of the transformer by optimizing the zero sequence current protection setting value, increasing no-load closing operation and interval time, and adopting inrush current suppression measures. This work is supported by National Natural Science Foundation of China (No. 51477090) and Science and Technology Project of China Southern Power Grid Company (No. GZHKJXM20160038).