In the substation of internal bridge connection, the main transformer operates in parallel with another transformer. Huge inrush current or fault current will flow through bridge breaker when one of the main transformers switches on or fault occurs. In that case, the differential protection of normal operating transformer may mal-operate because of the transient characteristic differences of current transformers and sympathetic inrush current. Considering a case of continuous mal-operations of differential protection, it is further analyzed and simulation validated on current transformer characteristic differences, phenomenon of sympathetic inrush current. Furthermore, it is calculated and analyzed on the ability of second harmonic to block the differential protection. Finally, the improved differential protection connection and some other measures are proposed to prevent differential protection from mal-operation.