A software-defined realization method based on a protection and control system for an intelligent substation, wherein merging unit and intelligent terminal integrated devices for all bays in the intelligent substation are directly accessed to transport ports on an intelligent power server, each of the merging unit and intelligent terminal integrated devices is accessed to a reception port of one of the transport ports on the intelligent power server through one optical fiber, and the each of the merging unit and intelligent terminal integrated device is accessed to a transmission port of the one of the transport ports on the intelligent power server through another optical fiber, wherein the transport ports and the merging unit and intelligent terminal integrated devices are in a relationship of one-to-one correspondence, the intelligent substation adopts a centralized modeling manner of adding and updating all of a protection function, a measurement and control function, an exchange function and a telecontrol function in substation configuration descriptions SCD files by taking the whole intelligent substation as a modeling object, the method comprises: through a SCD file configuration tool, creating the SCD files of the intelligent substation based on the merging unit and intelligent terminal integrated devices and each of special functions planned by the intelligent substation, and setting configuration information of each special function in the SCD files of the intelligent substation, wherein each of the special functions of the intelligent substation is set according to application scenarios of the intelligent substation; generating configured intelligent electronic device description CID files of the intelligent power server, by the intelligent power server, based on the SCD files of the intelligent substation; parsing the CID files of the intelligent power server by the intelligent power server to obtain the configuration information of each of the special functions; and realizing, by the intelligent power server, all of the measurement and control function, the protection function, the exchange function and the telecontrol function in the intelligent substation based on the configuration information of each of the special functions and sampled value SV messages and generic object oriented substation event GOOSE messages transmitted by the merging unit and intelligent terminal integrated devices. through a SCD file configuration tool, creating the SCD files of the intelligent substation based on the merging unit and intelligent terminal integrated devices and each of special functions planned by the intelligent substation, and setting configuration information of each special function in the SCD files of the intelligent substation, wherein each of the special functions of the intelligent substation is set according to application scenarios of the intelligent substation; generating configured intelligent electronic device description CID files of the intelligent power server, by the intelligent power server, based on the SCD files of the intelligent substation; parsing the CID files of the intelligent power server by the intelligent power server to obtain the configuration information of each of the special functions; and realizing, by the intelligent power server, all of the measurement and control function, the protection function, the exchange function and the telecontrol function in the intelligent substation based on the configuration information of each of the special functions and sampled value SV messages and generic object oriented substation event GOOSE messages transmitted by the merging unit and intelligent terminal integrated devices.