A hybrid energy storage system (HESS) composed of a battery and super-capacitor (SC) can make full use of advantages in energy and power density, which can further improve the performance of hybrid electric vehicles (HEV). Most studies have been limited to configuration and control to reduce the burden and prolong the life cycle of the battery, seldom focusing on the redesign of energy management strategies (EMS) for HEVs when passing from battery-only energy storage to HESS. In this paper, the equivalent fuel consumption during parallel-charging of a semi-active HESS in a series-parallel HEV under rule-based EMS was deduced, and a fuzzy-logic based (FLB) CS for the HESS was established using the state of energy (SOE) of the battery and SC as inputs. This allows the requirement of energy balance for HESS to be clearly expressed. Furthermore, the regulated EMS for HEV, which could dynamically manage the high efficiency of the engine and maintain the real-time charging/discharging capability of HESS, was proposed and verified under hardware in a loop test (HIL). Quantitative comparison of results between HESS and battery-only indicated that velocity-based SC’SOE-adjustable EMS presented in this paper could make better use of SC in filtering than SOE-constant EMS, and improve the fuel economy of HEVs from 22.76 l/100 km (battery-only) to 21.18 l/100 km. In order to emphasize the advantages of management, the electric energy usage/loss and efficiency under city driving-cycle were also presented.