With the rapid growth of electric vehicles (EVs) in recent years, the research on their energy storage systems (ESSs) has also shown great popularity. A traditional ESS normally has a fixed configuration and uses a single type of energy storage unit. However, this traditional design has some limitations, such as low flexibility and high requirements to unit consistency. To solve these problems, a new hybrid energy storage system is proposed in this paper. The proposed ESS hybridises multiple lithium-ion battery modules and one supercapacitor module. By controlling the states of switches inside the ESS topology, module level reconfiguration can be achieved. Further, a DC/DC converter is also included in the ESS topology, which is connected to the supercapacitor module and can be used to ensure correct ESS output voltage. Reconfiguration and active balancing algorithms are also given based on the proposed ESS topology. Situations with and without bypassing the lithium-ion battery modules are both discussed in the algorithms. The proposed hybrid ESS is finally verified with simulations. The system model is built in the Simulink/MATLAB environment. Simulation results show that the lithium-ion modules with a lower state of charge values have higher priorities to be connected in parallel. Reconfiguration actions are able to balance all lithium-ion battery modules within one Worldwide Harmonised Light-Duty Vehicle Test Cycle (WLTC) simulation cycle while maintaining ESS output voltage within a correct range. Furthermore, the proposed hybrid ESS control algorithms remain valid when one lithium-ion battery module is manually bypassed during simulation.