Multi-level energy management system (EMS) is proposed for dc microgrids operations to ensure system reliability, power quality, speed of response, and control accuracy in this paper. System distributed control is scheduled as the primary control. Battery energy storages (BESs) operate in voltage regulation mode with droop control for power sharing. However, bus voltage deviation and power tracking error due to line impedance are the main drawbacks of distributed control. To enhance the system power quality and control accuracy, bus voltage restoration and power sharing compensation are implemented in secondary control. Economic dispatch based on comparison of system units' marginal operation costs is carried out in tertiary control to minimize the system operation cost. Detailed elaboration has been derived to quantify BES utilization cost due to the cumulated lifetime degradation. In case of communication failure, system operation can still be retained with primary control without operating mode change so that to enhance system reliability. A lab scale dc microgrid is developed for the verification of the proposed multi-level EMS and relevant control techniques.