Coupling electric vehicles (EV) and hybrid energy storage (HES) with the distributed energy system (DES) can improve energy-saving and emission reduction efficiency and reduce system investment operating costs. However, the system modeling, optimization design, application site, and comprehensive performance analysis of the novel DES need to be further studied. Therefore, this paper combines photovoltaic technology, HES with P2G technology, and EVs with DESs to form a DES that combines HES. Taking the annual net energy import volume and annual cost as targets, a two-layer collaborative optimization method considering both system optimal configuration and operation strategy is used. The novel system will be used to supply energy to a nearly zero-energy community. The influence of various parameters is discussed through parameter analysis. The results show that under the operation strategy in charging during the daytime, the annual net energy import and annual value cost of the novel system are 2170772 kWh and 2272786 yuan, respectively; compared with the multi-parameter collaborative optimization method, it decreased by 3.1% and 5.0%, respectively. Finally, the two-layer collaborative optimization method of this paper is also applicable to the collaborative optimization design of other complex energy systems. The proposed operation strategy is also suitable for other energy systems with source, load, and storage.