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Based on the pursuit of different goals in the operation of the microgrid, it is not possible to meet the lowest cost and the least pollution at the same time. From the perspective of economy and environmental protection, a microgrid model including photovoltaic power generation, wind power generation, micro gas turbine, fuel cell and energy storage device is proposed. This paper establishes a comprehensive benefit objective function that considers both microgrid fuel cost, maintenance management cost, depreciation cost, interaction cost with public grid and pollutant treatment cost. In order to avoid the defect that the traditional particle swarm optimization algorithm is easy to fall into the local optimal solution, this paper uses the combination of simulated annealing algorithm and particle swarm optimization algorithm to compare with the traditional particle swarm optimization algorithm to obtain a more suitable method for microgrid operation. Finally, a typical microgrid in China is taken as an example to verify the feasibility of the algorithm.