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The mal-operation of transformer differential protection will occasionally take place after the removal of external fault due to current-transformer (CT) saturation. Study show that CT saturation can be divided into three kinds. Firstly, the influencing factors of CT saturation and effect of CT saturation to transformer differential protection are studied. Secondly, this paper analyzes the characteristic of the operating point when differential protection is mal-operated because of CT saturation. At last a method of different time delay in different areas is presented to prevent the differential protection from mal-operation. Simulation results validate its feasibility and reliability. It is significant if the method is realized for transformer protection.