The paper analyzes the reasons of the refusal operation of 220 kV bus differential protection. Its refusal operation occurs when the 220 kV breaker of 220~500 kV main transformer is replaced by bypass breaker, and a fault occurs in the other side of the main transformer with the 220 kV bypass breaker failure. According to the site situation, methods to improve the protection program and the secondary circuit are proposed to avoid the incorrect operation in such particular case.