Bipolar DC microgrid (MG) based on two voltage levels with three wires has higher reliability and flexibility than unipolar DC MG. However, the voltages of bipolar buses are coupled and the voltage of the PN bus affects the voltages of the bipolar buses in bipolar DC MG. In this paper, a hierarchical control with voltage balancing and energy management based on the characteristics of bipolar DC MG is proposed. To perform distributed power sharing with coupled voltages, droop-based primary controls for three buses and the coupling relationships between three buses are analyzed. Furthermore, in secondary control, balancing and voltage restoration controls are proposed to compensate for voltage drops caused by the balanced and unbalanced loads. To design the proposed hierarchical control, the stability analysis is performed. Additionally, a tertiary control based on an artificial neural network (ANN) is proposed for state-of-charge (SoC) management of bipolar DC MG. Experimental results of the proposed hierarchical control are verified by a lab-scale bipolar DC MG and performance analysis is performed with experimental and ideal results.