The zero sequence inrush of transformer is no longer biased on the side of the time axis ,and its secondary and three harmonic contents are higher. Compared with ordinary structure transformer, the high-voltage built-in transformer has smaller mutual leakage inductance and larger self-leakage inductance in structure parameters because its high-voltage side near the core. In addition, the high-voltage built-in transformer can produce larger amplitude, higher zero-sequence containing rate and slower attenuation of inrush current. By simulating the influence of different factors on inrush current characteristics, the conclusion that high-voltage built-in transformer is more likely to cause zero sequence current protection maloperation is obtained, and the preliminary countermeasures are given according to practical experience.