Aimed at the problem that the high harmonics generated by high frequency components in wind power system will affect the operation of substation main transformer protection, a method of transformer longitudinal impedance virtual phase protection is proposed. This method calculated the phase difference of the virtual longitudinal impedance on both sides of the fault component after the voltage translation, and then built a model on the power system computer aided design (PSCAD) platform for simulation and verification. By comparing the voltage data link, it can be seen that when an internal fault occurs, the virtual phase difference is greater than 90°; when an external fault occurs, the virtual phase difference is less than 90°. Finally, the simulation results show that the virtual phase difference changes from 0°to 180°, which is much greater than 90°; when the fault occurs in the area, the protection acts. In case of external fault and other factors that may affect the reliability of protection, the variation range of virtual phase difference is only 0°~20°, far less than 90°, and the protection does not act. Therefore, the following conclusions can be drawn from theoretical analysis: internal faults can operate reliably; In case of external fault, current transformer (CT) saturation and excitation inrush current, the protection does not act even under the influence of harmonics. At the same time, the error accuracy of existing CT can meet this protection method. The simulation results are consistent with the theoretical analysis, and verify the correctness and reliability of the protection under the existing CT accuracy and the better anti CT attenuation capability.