The invention discloses a third-generation intelligent substation measurement and control sub-machine test system and an application method thereof. The third-generation intelligent substation measurement and control sub-machine test system comprises a chassis and a mainboard module, a high-availability seamless redundancy (HSR) message communication module, a communication plug-in and a power source module which are separately installed in the chassis. The application method comprises the steps of using the third-generation intelligent substation measurement and control sub-machine test system to complete the automatic point-to-point test of the position telecommand of a measurement and control sub-machine isolator and the automatic point-to-point test of a guidance command. The third-generation intelligent substation measurement and control sub-machine test system realizes the simulation analysis of the HSR protocol of the measurement and control sub-machine, provides a novel closed-loop automatic testing scheme for the automatic testing and overhaul of the switching quantity-to-point function of the measurement and control sub-machine, greatly improves the overhaul and maintenance efficiency of a third-generation intelligent substation, and ensures safe and reliable operation of a power grid.