UHV AC substation auxiliary power system usually adopts two-stage step-down approach, and level 2 series transformer differential protection needs to be led by the CT of 110 kV and 380 V side current. When low voltage side failure occurs, the low voltage side current dozens thousand amperes, converting it to the high side, it is only a few hundred amperes. Because of the large difference on both sides of the current data, it brings some problems on CT model selection and configuration, principle, and setting of station transformer protection. Through the study of the configuration and connection mode of low voltage side of 1000 kV UHV Huainan substation equipment, combined with the actual engineering conditions and equipment parameters, this paper analyzes the UHV AC substation station with transformer protection special problems, puts forward the technology solution that a set of protection device is configured in the double set of current conversion module and two sets of differential protection and backup protection, and establishes a dynamic model system to verify the feasibility of this principle scheme.