This paper proposes a method to estimate the appropriate minimum output of diesel generator in the microgrid system that composed of renewable energy, diesel generator and energy storage systems. While maximizing the output ofthe renewable energy in the microgrid, to maintain the power system stability is very important. To analyze the effectiveness of the proposed method, simulation is carried out by using the PSCAD/EMTDC program with past weather and power load data in Chuja Island located in the south area of Korean peninsula, respectively. In the simulation result, power quality of Chuja Island power system under variable renewable energy generation is stable. The proposed method is useful for operating the isolated microgrid system.