When parallel converter structures are considered in modern DC distribution systems, several challenges are faced in the energy management system (EMS). For example, the circuit parameter mismatches of parallel isolated DC-DC converter modules will cause power imbalances, which is the most important concern in DC distribution system. To deal with this issue, this study presents a power management control scheme in the EMS to ensure the power balance of isolated DC-DC converters in DC distribution system. In the proposed method, the proposed shifted voltage is introduced at the output of each converter to compensate the output impedance mismatches. Especially, the shifted voltage is flexibly determined according to the output current sharing error to obtain a balanced output impedance among converters, and the balanced power sharing is achieved by means of the modified voltage reference. The simulation results with the stand-alone DC distribution system are carried out to verify the effectiveness of the proposed control scheme.