A simulation model based on MATLAB is developed to analyze the mal-operation of differential protection in voltage regulating transformer（VRT） in an experiment project of ultra-high voltage system， which is caused by inrush current during energizing of the transformer from medium-voltage side. According to particular structure of ultra-high voltage transformers， the influence of closure angle and residual magnetism， etc. on inrush current is analyzed and the waveform of field failure is resembled with simulation. In order to solve mal-operation caused by less second harmonic in differential current of VRT， lock criteria for second harmonic of inrush current should adopt two-out-of-three principle， but it may not valid in some situation. Furthermore， auxiliary criteria with second harmonic tendency is proposed for identifying inrush current or faulty current. Besides， it analyzes the influence of VRT capacity on inrush current and also suggests that suitably increasing the capacity of VRT should be considered in order to avoid mal-operation resulted from inrush current， if possible. The simulation results verify that the improved scheme is able to effectively avoid mal-operation of differential protection from inrush current.