Disclosed is a method for configuring the energy storage capacity of an autonomous micro-grid. The method is based on the autonomy of the micro-grid, a configuration target includes that energy deficiency accumulated in operating procedures is compensated by an energy storage portion and surplus energy is absorbed by the energy storage portion, the requirement on the capacity for the energy storage portion to stably run for an expected time under extreme conditions of a system is taken into consideration, and the method for configuring the capacity relevant to the permitted longest continuous running time T of an island of the micro-grid and the expected stable running time T2 of the micro-grid under the extreme conditions of the micro-grid is provided. The method has the advantages that the capacity of the energy storage portion of the micro-grid can be configured according to specific index requirements, and the method is high in pertinence and practicality.