Coelogyne pandurata Lindl. is an endemic orchid species of Indonesia from East Kalimantan and Papua. It is locally known as the “black orchid” due to the distinctive black coloration on its labellum with intricate green and hairy lines. Unfortunately, the population of this orchid has significantly declined in its natural habitat, rendering it a rare endangered species. Temporary immersion bioreactor systems have been proven to be efficient for endemic plant micropropagation with performance enhancements and innovations. This study aims to develop an optimized bioreactor design and innovate the automatic control performance of temporary immersion bioreactor systems based on previous research. The control system developed consists of three modules, namely Graphical User Interface (GUI) module, Sequence Control (SC) module, and Hardware Interface (HI) module. The GUI module receives information regarding time and duration of immersion and gas exchange, then the information is synchronized by the SC module, which plays the role of starting and stopping the processes, while HI module executes the order of the automatic control system in the immersion and gas exchange process. The developed bioreactor design and control system offer convenience, require less labor, and ensure precise control over the optimum conditions for black orchid micropropagation.