The invention discloses a double-redundancy microgrid energy scheduling safety chain system and a control method thereof. The system comprises power electronic equipment connected to the microgrid and an energy scheduling system communicating with the power electronic equipment, a safety chain collection unit is arranged in a communication link between the power electronic equipment and the energy scheduling system, and sends data to a safety chain control unit, and the energy scheduling system comprises an energy scheduling controller which communicates with the safety chain control unit. According to the system and method, the safety chain collection unit collects data of the power electronic equipment, and verifies a mutual comparison mode of the energy scheduling system, when verification has a problem, intelligent analysis is made, analysis results are classified, the robustness of the whole control chain is determined, and related stability protection is completed.