Because of huge current in low voltage side of an isolated transformer，it is difficult to select a matched current transformer and apply sensitive current differential protection to the isolated transformer.In order to provide more sensitive protection to the isolated transformer，power flow controller（PFC）and the electric cables between them，the relation of fundamental input active power to output active power of cophase supply equipments is analyzed theoretically.Based on balance of active power，an active power differential protection（APDP）scheme is presented.Moreover，the operation behaviors of APDP are analyzed under many conditions，such as the isolated transformer energizing，PFC initiation，normal operation，external fault，internal fault and so on.The setting principle of APDP for cophase supply equipments is discussed，and a real instance is also given.The test results in lab and project field show the validity of APDP.