The invention relates to a controller based on a scenario test of secondary equipment of an intelligent substation. The controller is technically characterized in that the controller comprises an ARM (acorn RISC machine) module, a DSP (digital signal processor) module and an FPGA (field-programmable gate array) module, wherein the ARM module is connected with the DSP module to achieve data transmission and data configuration functions; the DSP module and the FPGA module output simulation data generated by the DSP module to the FPGA module; the ARM module is provided with two electric Ethernet interferences connected with an upper computer and a protection device; the FPGA module is provided with an optical Ethernet interference connected with GOOSE (generic object oriented substation event), IEC61588, IRIG-B (inter-range instrumentation group) and an intelligent electronic device; the FPGA module is provided with an optical serial port connected with a combiner, and the FPGA module is provided with an input quantity interface and an output quantity interface which are connected with the protection device. The controller is reasonable in design, and matched with the upper computer to achieve a simulated closed-loop test of an operation scenario of the secondary equipment of the intelligent substation, provides a test method for detection of a fault of the secondary equipment of the intelligent substation and an SCD (substation configuration description) file of the entire substation, and guarantees reliable operation of the system.