This paper deals with the real-time energy management strategies for a hybrid energy storage system (HESS), including a battery and a supercapacitor (SC), for an electric city bus. The most attractive advantage deriving from HESSs is the possibility of reducing the battery current stress to extend its lifetime. To quantitatively compare the effects of different control strategies on reducing battery degradation, a dynamic degradation model for the LiFePO4 battery is proposed and validated in this paper. The battery size is optimized according to the requested minimal mileage, while the size of SC is optimized based on the power demand profile of the typical China Bus Driving Cycle (CBDC). Based on the optimized HESS, a novel fuzzy logic controller (FLC) and a novel model predictive controller (MPC) are proposed and compared with the existing rule-based controller (RBC) and filtration based controller (FBC), after all the controllers are tuned to their best performance along the CBDC. It turns out that FLC and RBC achieve the best performance among the four controllers, which is validated by the DP-based result. Furthermore, about 50% of the HESS life cycle cost is reduced in comparison with the battery-only configuration. In addition, the controllers are also compared along the New European Driving Cycle (NEDC), which represents another normalized driving cycle. The results show that the RBC, MPC, and FLC achieve a similar performance, and they reduce about 23% of the HESS life cycle cost when compared to the battery-only configuration. The RBC and FLC are regarded as the best choices in practical applications due to their remarkable performance and easy implementation.