This paper presents the system integration and hierarchical control implementation in an inverter-based Microgrid Research Laboratory (MGRL) at Aalborg University, Denmark. MGRL aims to provide a flexible experimental platform for comprehensive studies of microgrids. The structure of the laboratory, including the facilities, configurations, and communication network, is first introduced. The complete control system is based on a generic hierarchical control scheme including primary, secondary, and tertiary control. Primary control loops are developed and implemented in digital control platform, while system supervision, advanced secondary, and tertiary management are realized in a microgrid central controller. The software and hardware schemes are described. Several example case studies are introduced and performed to achieve power quality regulation, energy management, and flywheel energy storage system control. Experimental results are presented to show the performance of the whole system.