The invention relates to a whole-group verification method and system for a network virtual secondary loop of an intelligent substation. The method comprises the following steps: acquiring a CID (Configured IED Description) file and an ICD (IED Capability Description) file of IED equipment to be verified and an SCD (Substation Configuration Description) file of the intelligent substation, and extracting configuration description specific to the IED equipment in the SCD file; extracting SV configuration and GOOSE configuration in the configuration description, and generating an SV test message and a GOOSE test message according to the SV configuration and the GOOSE configuration; receiving a test parameter input by a user, extracting equipment characteristics in the configuration description, and generating a protection logic verification message; sending the messages to the IED equipment respectively; and receiving an action message returned by the IED equipment to be verified, and judging that the IED equipment to be verified works normally if the action message is consistent with a pre-stored action reference message. Through adoption of the whole-group verification method and system, the complexity degree of the secondary loop in an intelligent power grid is lowered; operation of periodical verification personnel is reduced; and power failure time in a whole-group verification process is shortened.