This paper presents a distributed hierarchical control framework to ensure reliable operation of dc microgrid (MG) clusters. In this hierarchy, primary control is used to regulate the common bus voltage inside each MG locally. An adaptive droop method is proposed for this level, which determines droop coefficients according to the state-of-charge (SOC) of batteries automatically. A small-signal model is developed to investigate effects of the system parameters, constant power loads, as well as line impedance between the MGs on stability of these systems. In the secondary level, a distributed consensus-based voltage regulator is introduced to eliminate the average voltage deviation over the MGs. This distributed averaging method allows the power flow control between the MGs to be achieved at the same time, as it can be accomplished only at the cost of having voltage deviation inside the system. Another distributed policy is employed then to regulate the power flow among the MGs according to their local SOCs. The proposed distributed controllers on each MG communicate with only the neighbor MGs through a communication infrastructure. Finally, the developed small-signal model is expanded for MG clusters with all the proposed control loops. The effectiveness of the proposed hierarchical scheme is verified through detailed hardware-in-the-loop simulations.