To reduce the carbon emissions of microgrid system operation and consider the influence of renewable energy output uncertainty on the system dispatching, a low-carbon economic dispatching model of the microgrid based on robust optimization is proposed. First, a two-stage robust optimization method is used to eliminate the impact of renewable energy output uncertainty on the system scheduling results. Second, a stepped carbon trading mechanism is introduced into the operation and scheduling stage of the system to reduce the carbon emissions of the microgrid. Then, a low-carbon economic dispatch model of the microgrid including a wind turbine, a photovoltaic unit, a micro gas turbine, a fuel cell, and an energy storage device is established. With the optimization objective of minimizing the sum of operation and maintenance costs of each piece of equipment, system energy purchase costs and carbon trading costs, the C&CG algorithm is used to analyze the proposed scheduling model. Finally, the proposed optimal scheduling model has been verified by a series of examples. The results show that the two-stage robust optimization method can effectively improve the ability of the system to resist risks and the introduction of a stepped carbon trading mechanism can effectively reduce the carbon emissions of microgrid operation.