Recovering regenerative braking energy is a very effective way to reduce energy consumption of urban rail transit system(URTS). In this paper, modeling and control strategy is studied for super capacitor(SC) and lithium titanate battery(LTB) hybrid energy storage system (HESS) applied in URTS. Based on modeling of subsystem of URTS with HESS, the paper proposes a multi-module coordinated control and management strategy of HESS, which not only meets the needs of regenerative braking energy recovery and utilization, but also considers the long-term operation management of SC and LTB, and is verified through simulation. For practical application, this paper developed a 1MW HESS prototype, and test verification in an actual line. The experimental results show that HESS and control strategy proposed in this article has a obviously effect in recovering and utilizing regenerative braking energy.