DC microgrids are characterized by attractive features such as high efficiency, reduced cost, suitability for distributed generation connection, and needlessness for synchronization. The control and operation of the DC microgrid become significantly important for its stability. This paper proposes a multi-level and multi-time-scale Hardware in-the-loop Simulation (HILS) system as a new method to develop and test control algorithms and operation strategies for the DC microgrid. According to different control hierarchies and time scales, DC microgrid primary control, secondary control and optimal operation control algorithm are implemented in different real-time simulators and controllers. The key unit and system control methods can be both tested in the proposed design. Finally, according to the proposed design and different processors’ computing ability and characteristics, the HILS platform including a DSP, a RT-LAB, a cRIO and a host computer is built. Detailed tests are carried out to show feasibility and flexibility of the proposed HILS platform. This work is supported by National High-tech R & D Program of China (863 Program) (No. 2015AA050101).