The Hydrogen Maser Clock (HMC) will provide a frequency standard in near-earth orbit with stability of one part in 1015 over a day. Originally scheduled for launch on EURECA, the flight-model HMC requires only mechanical interface adapters and access to a heat sink to operate on a wide variety of space platforms.Because the oscillation frequency of the hydrogen maser at the core of the experiment is a strong function of temperature, control of the maser to about 10-4°C is required to achieve the needed stability. This paper addresses co-evolution of both thermal design configuration and feedback control system design. Thermal design details presented include choice of materials and heat flow paths, placement of sensors and heaters, thermal gradient control, and effects of thermal response time. The controller design discussion incorporates bridge amplifier stability, effect of analog-to-digital quantizing, multi-zone microprocessor thermal control, and tuning the system for performance. Finally, we discuss testing of engineering and flight instruments to demonstrate successful control over a range of external environment changes.