Battery/Supercapacitor(SC) current tracking control is a key issue for hybrid energy storage system (HESS) in electric vehicles. An innovative passivity-based L2-gain adaptive control (PBL2AC) based on port-controlled Hamiltonian model with dissipativity (PCHD) for reference current tracking and bus voltage stability in HESS is presented. The developed PCHD model has considered both parameter variations and external disturbances. By using L2-gain disturbance attenuation, the PBL2AC ensures robust reference current tracking and stable bus voltage. Moreover, adaptive mechanism is adopted to estimate the electrical parameters. To validate the proposed control scheme for HESS, simulations and experiments were done and compared with traditional PID and sliding mode control under several typical driving cycles, and results show that the effectiveness of the proposed controller can be confirmed.