The phase segregated（zero sequence） differential relay for auto-transformer is principally not affected by transformer magnetic inrush. However the relay mal-operations happened occasionally on domestic made three phase compact auto-transformers during their no load energizing. The causes of relay mal-operation are found to be abnormal transformation of common winding current transformer other than the relay operation principle itself after several cases studied. Furthermore， based on the comparison of the energizing current shape data between domestic made transformer and joint venture made ones， it is concluded the characteristics and saturation of common winding current transformer are not problems. With structure analysis of auto-transformer， it shows that the influence of leak flux rising from transformer energizing on common winding current transformer is not considered in domestic made auto-transformers. Therefore improvement measures for relay operation criteria are put forward on the basis of analyzing results. Finally it suggests that transformer manufacturers study and improve the transformer internal structure in order to completely solve the abnormal transformation of common winding current transformer.