Phase differential and zero-sequence differential protection for auto-transformer cannot be affected by magnetizing inrush current，but protection for the three-phase compact auto-transformer made in China sometimes mis-operates when energizing.By comparing the energizing current waveforms of domestic or joint-venture330kV three-phase compact auto- transformers，it has been found that the main reason for the mis-operating of domestic ones is that the saturation of common winding current transformer core will lead to the abnormal current transformation.It is further studied that the essential factors for the abnormality exist in the internal structures and materials of auto-transformers，which need to be improved. Finally，the analysis is verified using the professional simulation software，ANSYS，based on the finite element method.