In conventional hybrid energy storage systems, two storage units complement each other. One low-capacity and fast-response unit as a power supplier, and one high-capacity and low-response unit as an energy supplier. The power supplier mitigates fast fluctuations in generation or demand by transferring energy over seconds or minutes, and the energy supplier transfers energy over hours for managing energy. According to this concept, this paper presents a new model of hybrid energy storage systems, where three energy suppliers are considered as a three-level hybrid energy storage system. Energy storage at level 1 shifts energy from off-peak (or low-cost) hours to the on-peak (or high-cost) hours during one day, the storage unit at level 2 transfers energy from off-peak (or low-cost) days to the on-peak (or high-cost) days for the period of one week, and level 3 transfers energy from off-peak seasons to the on-peak seasons through one year. The proposed planning results in a large-scale optimization programming that optimizes large numbers of design variables at the same time. In order to increase the flexibility of the planning, the initial energy of the storage units is also modeled as a design variable and optimized. The uncertainty of loads is modeled and a stochastic planning is carried out to solve the problem. The introduced three-level hybrid energy storage planning is simulated on two test systems, and the results demonstrate that the proposed planning can reduce the planning cost by about 1.8%.