This study looks into the power flow control of a battery/super capacitor hybrid energy storage system when applied to electric vehicles. The controller is based on advanced model predictive control method and aims at smoothing the power flow from/to the battery to protect it from undesirable fast discharging/charging. The second objective of the controller is to control the electric vehicle to track a predefined speed profile. The dynamics of the vehicle and the super capacitors are modeled from first principles to facilitate the controller design. It is assumed that the battery, as the primary energy source for the vehicle, is properly sized such that there is no need to control its state-of-charge. In addition, the controller is designed at the energy management level instead of power electronics control level. Therefore, it severs to optimize the power flows of the hybrid energy storage system instead of controlling the power converters involved. Simulations based on two commonly used urban driving cycles are carried out to verify the effectiveness of the design.