Distribution generation（DG） technology has been rapidly developed and the DG penetration level is becoming higher and higher in the distribution system in recent years. The magnitude， direction and distribution of the short circuit current in distribution power system have changed a lot due to the introduction of DGs. This has brought several problems to the traditional staged over current protection devices and may cause them mal-operation. To satisfy the requirements and resolve the existing problems of the relay protection of the distribution systems under high DG penetration level， a new protection scheme is introduced. The new protection scheme is based on longitudinal comparison principle. With the foundation of communication technology， the new scheme is a kind of substation area longitudinal protection with master-slave structure， for the purpose of protecting the whole distribution substation and all of its outgoing feeders that are under high DG penetration level. The operation procedure and fault location method of the protection system is described.