High-speed railways generate a large amount of regenerative braking energy during operation but this energy is not utilized efficiently. In order to realize the recycling of regenerative braking energy of high-speed railways, the hybrid energy storage type railway power conditioner (RPC) system is proposed. The working principle and the control strategy of the system are studied. The energy management strategy consisting of a hybrid energy storage system charging and discharging strategy and variational modal decomposition (VMD) power allocation strategy is proposed. Three system operation modes are proposed: the power of the hybrid energy storage system is decomposed by VMD and an interrelationship number is proposed to determine the lithium battery and supercapacitor power. The hardware-in-the-loop test experiments are conducted by the StarSim power electronics small-step real-time simulator from Modeling Tech and the validation analysis is carried out on MATLAB/Simulink with the actual measurement data of a traction substation on the Lanzhou–Xinjiang line. The results verify that the proposed strategy can effectively recycle the regenerative braking energy, realize the peak-shaving effect on the load, and reduce the energy consumption of the train.