Along with the development of high switching frequency power electronics, the research and application of DC Solid State Transformer (DCSST) is getting more and more attention. But because of the high frequency characteristic of DCSST, the CPU based real time simulation which typical computation time-step is about the scale of 10 μs can’t reflect the high frequency characteristic of DCSST precisely, given this, FPGA based real time simulation is proposed, because of the parallel computation characteristic of FPGA, its computation time-step can be up to scale of nanoseconds, so FPGA can simulate the high frequency characteristic of DCSST accurately. In this paper, the topology of DCSST and its FPGA based model are presented, and related control algorithm is proposed. Real time simulation results verify the feasibility and effectiveness of FPGA based DCSST real time simulation and the related control algorithm.