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As an effective carrier for integrating distributed photovoltaic (PV) power, the microgrid system is one of the most effective ways to realize the on-site consumption and utilization of distributed photovoltaics. In order to ensure the reliability of the power supply of the microgrid system and maximize the utilization and economic of the photovoltaic, it is necessary to appropriately configure energy storage for the rural microgrid system. This paper studies the photovoltaic and energy storage optimization configuration model based on the second-generation non-dominated sorting genetic algorithm (NSGA-II), by comprehensively considering the load characteristics, local environmental factors and various economic factors such as pollutant reduction benefits in a rural area. The analysis case presented in this paper is based on the operation data of a microgrid in a rural area in Guangdong province, China. The results show that the optimized photovoltaic and energy storage system can effectively improve the photovoltaic utilization rate and economic of the microgrid system. The model can provide an effective method for the design of photovoltaic and energy storage configuration schemes for microgrids in rural areas.