HARMONI is the Extremely Large Telescope visible and near infrared integral field spectrograph and will be one of the first light instruments. The instrument supports four operational modes called No Adaptive Optics (NOAO), Single Conjugated Adaptive Optics (SCAO), High Contrast Adaptive Optics (HCAO), and Laser Tomography Adaptive Optics (LTAO). These operational modes are closely related to the wavefront correction topology used to support the performance required for each of the science cases. By following a novel function model-based systems engineering (FBSE) methodology in conjunction with observing the software computer system golden rule of design; namely having tight cohesion within software modules and loose coupling between modules, a system architecture has emerged. In this paper, we present the design of the HARMONI Control System (HCS). Although this is not the first time (for example NACO on VLT and NIRC2 on Keck) that the adaptive optics required to correct the atmospheric turbulence is part of a general instrument design, and not tailored for a very specific science case, this will be the first instrument of this size and complexity in the era of extremely large ground-based telescopes. The instrument control design must be compatible with the ELT instrument control system framework while there is also an expectation that the adaptive optics (AO) real-time computer toolkit (RTC-TK) should be used for the realization of the AO real-time control software and hardware. The HCS is composed of the instrument control electronics (ICE), the Instrument Control System (ICS), and the AO Control Sub-system (AOCS). The operation concept of the instrument is also novel in that for each mode the instrument creates an instantiation of a virtual system composed of only the system blocks required to provide the selected mode of operation. Therefore, each mode supports a unique system composition in terms of hardware, software, and the sequencing of activities.