An energy management system for enhancing design and operation of a distributed energy resource system includes a two-level design system and a hierarchical optimization-based control system. The two-level design system includes a top-level designer configured to coordinate decentralized bottom-level designers for individual energy resources to seek a global target for the designed distributed energy resource system that satisfies the energy demand of a target deployment location within a confidence level, and multiple bottom-level designers configured to enhance detailed designs of local energy sub-systems. The hierarchical optimization-based control system include a primary controller configured to determine a long-term operational schedule based on long-term constraints and future events at a first level, one or more secondary controllers configured to control daily orchestrations of the distributed energy resource system during operation at a second level, and multiple tertiary controllers and aggregators configured to rapidly adjust various hardware at a third level.