The invention provides an intelligent substation configurable relay protecting method and system. The method includes: configurable relay protection is configured, and a configuration central server is configured in a secondary system, wherein the configuration central server is a control center using primary network state as a constraint condition to perform secondary equipment function cutting and combination; during system operation, the configuration central server manages and dispatches the functions of IED equipment, performs monitoring and state analyzing on the equipment of the primary system and the secondary system, controls the logic nodes of each IED equipment according to analyzing results, cuts and combines of the logic nodes to obtain function-configurable and variable virtual IED equipment, and performs protection control according to the virtual IED equipment. The method has the advantages that the method is flexible in protecting function, integrated in information and applicable to occasions such as backup protection, function migration and plug and play, safety and reliability of a relay protecting system are effectively increased, and convenient operation and maintenance and convenient control are achieved.