The phase-shifting transformer is a piece of economical power flow regulation equipment. It can improve the safety and economy of power grid operation. To realize the engineering application of a tap-changer controllable phase-shifting transformer, first, a main protection configuration scheme of a phase-shifting transformer is proposed from the configuration of current and voltage transformers, and the protection range of each protection element is analyzed. Secondly, a differential adaptive adjustment strategy based on the coordination of control and protection devices is proposed. This can provide that the differential protection calculation of the phase-shifting transformer can be adjusted adaptively according to the real-time tap position of the tap-changer. Then, a current calibration method based on the differential balance of the phase-shifting transformer is presented. This can be used to verify the polarity and parameter of each current transformer. Finally, the waveform characteristics and the adaptability of protection with different fault types and no-load switch-on scenario are analyzed by simulation and real waveform, and the effectiveness of the proposed methods and protection configuration are proved.