Abstract: When the high-voltage built-in high-impedance transformer is no-load excited, a high-amplitude but slowattenuation magnetizing inrush current will arise. It may cause the maloperation of bus tie zero-sequence over current protection, and then the transformer fails to be switched on. To solve this problem, waveform characteristics of zero-sequence inrush was analyzed and it can be concluded that there is high second harmonic component and it increases with time. Then the second harmonic component was introduced in bus tie zero-sequence current protection to identify zero-sequence inrush. Besides, it was considered that the traditional second harmonic break ratio cannot identify CT saturation, so the scheme based on second harmonic component was improved. A new zero-sequence over current protection method based on second harmonic component and its changes characteristic was proposed. The scheme was equipped with anti-CT saturation performance. At the same time, the characteristics of discrete data in microcomputer protection were considered as well, which is convenient for engineering applications. Finally, the operation of the scheme in different scenarios is verified by PSCAD/EMTDC, which is in line with expectations.