The invention provides a secondary device integration and joint debugging method based on a virtual machine. The method comprises the steps that S1 the minimum test system of an intelligent substation is built according to the principle of guaranteeing the substation consistency; S2 the real test environment of the substation is built based on the minimum test system; by importing an SCD file, the configuration of the devices of the whole substation is acquired; data flows including SV flow and GOOSE flow in each device are acquired; the model of the whole substation is built through backstage, and the information of the devices of the whole substation is scanned; and S3 the minimum test system is used to integrate the device information and the definition and definite value of action behaviors to acquire a test item, a test program and a test result template. The factory-like joint debugging efficiency is improved. The joint debugging intelligent level is enhanced. The device debugging cycle is shortened, and the debugging environment is improved.