The load characteristics of high-speed railway systems have an adverse effect on the three-phase symmetry of the power supply system. A back-to-back converter connected in series to a supercapacitor energy storage device is used to solve the three-phase imbalance problem and the regenerative braking energy recovery problem of trains that occurs during the operation of the railway system. An improved particle swarm algorithm is used to optimise the access capacity of the back-to-back converter. The mechanism of negative sequence complete compensation of the energy storage type railway power conditioner when the grid voltage is unbalanced is analysed, the compensation coefficient of the energy storage system, the active and reactive current compensation coefficients are introduced, the degree of negative sequence compensation and the compensation capacity of the traction substation and the load balance of the supply arm are taken as the optimisation objectives, and the optimised compensation model of the energy storage type railway power conditioner is proposed. Simulation analysis of the newly accessed circuit structure model shows that the model can make full use of the regenerative braking energy of electric locomotives, compensate the negative sequence current introduced into the three-phase grid by the traction system and reduce the energy demand of the traction transformer by the traction load.