In order to improve the comprehensive energy utilization rate of combined cooling, heating, and power (CCHP) system, a hybrid energy storage system (HESS) is proposed in this paper consisting of electric and thermal energy storage systems. And the overall optimization design and operation of CCHP system with HESS are the main problems to be solved in application. Therefore, the topology and the energy flow model of CCHP system with HESS are established and analyzed according to the energy conversion characteristics of the component equipment. Moreover, combined with five evaluative restrictions for HESS system, a rule-based energy management strategy is designed to realize the decoupling regulation of electric energy and thermal energy in CCHP system. On this basis, a multi-objective optimization model is studied by taking the indicators of annual cost ratio, the primary energy consumption ratio, and loss energy ratio, and then the capacity parameters are optimized by particle swarm optimization algorithm (PSOA). Finally, a case is carried out to compare the energy allocation situations and capacity optimization results between CCHP system with HESS and CCHP system with single thermal energy storage system (ST). Results show that the capacity of ICE is reduced by 34%, and the annual cost and the primary energy consumption are saved about 7.69% and 18.47%, respectively, demonstrating that HESS has better optimization effect and applicable for small-scale CCHP system.