The invention discloses a method and a device of secondary equipment associating configuration. The method includes adding key function logic node configurations in a primary equipment object model of an intelligent substation; establishing a standard knowledge base of secondary equipment types and models of the intelligent substation, wherein the standard knowledge base contains secondary function key function logic node configurations; establishing a system specification description file of the intelligent substation comprising a secondary function knowledge base configured correspondingly to the primary equipment of the intelligent substation; performing associating configuration by means of key function logic nodes in the secondary function knowledge base and key function logic nodes corresponding to the standard knowledge base according to the system specification description file and a system configuration description file, and configuring the secondary equipment via the configuration relation of the key function logic nodes. By the method, integrative configuration of projects of the intelligent substation can be simplified, and workload in system configuration is reduced.