Zero-sequence current differential protection for grounding fault has the advantages of high sensitivity, action current’s independence with transformer tap joint, small influence from inrush current, and principle simplicity. It is widely used in the area of UHV autotransformer protection. However, the zero-sequence current differential protection operates due to responding to the phase sum of zero sequence current in three sides of autotransformer, which is badly influenced by the saturation of current transformer and hard to set the threshold. In the external fault, it will lead to mal-operation. Based on this, a new auto-transformer pilot protection scheme based on the zero-sequence current phase comparison is proposed. The fault direction can be determined by comparing the phase shift between zero sequence current of high voltage side, medium voltage side and the reference current. So the internal fault and external fault can be discriminated. The results of dynamic simulation experiment and digital simulation shows that the proposed method can detect turn-to-ground and turn-to-turn fault with high sensitivity and good selectivity. Besides, the protection criterion is not affected both by the non-periodic component of zero-sequence current and saturation level of fault-side current transformer (CT).