The protection behavior in a circuit breaker fault is analyzed, and it shows that there are serious defects in the configuration scheme of current transformer used by protection in smart substation. When a set of protection is out of operation, the protection dead-zone will occur and the removal of fault is heavily dependent on breaker failure protection with time delay. Worse still, the breaker failure protection will fail to operate because the fault current can not be detected correctly, which severely threatens to the security of the power system. To solve this problem, a novel configuration scheme of current transformer with two TPY coils and one P coil in every break is proposed from engineering design to eliminate the protection dead zone thoroughly. In addition, remedial measures such as disconnecting the associated breakers from system operation and installing dead-zone protection or modifying breaker failure protection from protection configuration are also put forward. These solutions have been successfully applied to the construction and operation of 750 kV smart substations in Northwest Power Grid of China, which improves the protection reliability and system stability.