In order to solve the problem that the economic cost and power supply reliability of independent microgrid capacity allocation are difficult to achieve simultaneously, a multi-objective optimal allocation method of independent microgrid capacity is proposed to achieve the optimal economic cost and power supply reliability. A mathematical model of a wind turbine, a photovoltaic and a lithium iron phosphate battery is constructed according to the mechanism of each distributed power supply in an independent wind-photovoltaic-storage microgrid system; an independent microgrid economic cost model is constructed by taking the equal annual investment cost as an evaluation index, and an independent microgrid reliability model based on an analytic hierarchy process is constructed by taking the power deviation as an evaluation index; Multi-objective particle swarm optimization with non-dominated sorting is used to solve the optimal capacity configuration of the system. The example results show that the proposed method is more advantageous in achieving both power supply reliability and economy for the capacity allocation of independent microgrid.