Considering the response characteristics of electric and thermal energy storage and the temperature control characteristics of thermal load, a method for allocating hybrid energy storage capacity in multi-energy microgrid is proposed to improve the reliability and economy of the system in this paper. Firstly, the net load index between new energy output and electric load is defined. Based on the difference of response speed between electric storage and thermal storage, the power distribution of electric and thermal storage is determined by discrete Fourier transform decomposition of net load power. Secondly, on the thermal load side, a temperature control model of thermal energy storage is established, considering the capacity of thermal storage system in concentrating solar power (CSP) and heat pump to regulate thermal load. Finally, considering the system investment cost, operation and maintenance cost, power shortage penalty cost and wind abandonment penalty cost, a multi-element hybrid energy storage double-layer capacity optimization model with minimum equivalent annual cost as the objective function is established. The outer layer of the model determines the energy storage power allocation by optimizing the Fourier subsection points, and then obtains the range of hybrid energy storage capacity. The inner layer uses mixed integer linear programming (MILP) to get the hybrid energy storage capacity allocation, which realizes the bi-level optimization of energy storage power allocation and capacity allocation. The economy and effectiveness of the proposed method are verified by a case study of an actual microgrid.