To better recycle the regenerative braking energy (RBE) and improve the power quality (PQ) in asymmetric AC-fed railways, a novel multiplex back-to-back energy storage system (MB2ESS) with fault-tolerance ability is proposed, where individual subsystems not only independently operate as self-controlled entities, but also collaborate with adjacent subsystems to resist system disturbances and local faults. On this basis, a hierarchical optimization control method with three-layer structure is designed for the flexible and effective operation of MB2ESS, including the global optimization layer based on finite state machine, the regional decision-making layer with event-driven distributed coordination controller, and the local execution layer via multi-converter autonomous control. It can be used to seamlessly switch different operation modes, coordinately manage the multidirectional transmission of RBE, dynamically control PQ optimization compensation, and rapidly perform fault response behaviors. Subsequently, through typical scenarios, comparative study, and field case of a traction substation in Beijing-Shanghai Railway, the feasibility and effectiveness of proposed scheme are verified. The engineering capability assessment results also show that this scheme can effectively make up for the structure and function deficiencies of conventional railway energy storage systems, which has well adaptability and application potential.