Aiming at the problem of power balance between the renewable energy generation and the load in the isolated mode, starting from the real-time control operation requirements, this paper proposes a capacity configuration scheme for energy storage systems based on the daily energy scheduling management and real-time error control. Firstly, by dividing the energy storage system into a main energy storage system and an auxiliary energy storage system, a multi-objective optimization function which takes into account both the cost loss of the energy storage system and the gas turbine generator configuration is established. The required main energy storage configuration is obtained by using the improved particle swarm optimization and the convergence principle, and the previous energy management schedule is completed at the same time. Then, the scene simulation method is used to obtain the capacity configuration of the auxiliary energy storage system which is needed to complete the real-time operation, and the corresponding control strategy is formulated to complete the real-time energy management. Finally, through the numerical simulation, the feasibility of the configuration scheme proposed in this paper is verified. Under the condition of satisfying the economy and practicality, the configuration of the microgrid in the whole isolated network mode is completed. This work is supported the National Natural Science Foundation of China (No. 61673174) and Shanghai Excellent Academic/Technical Leader Plan (No. 16XD1421300).