Objectives: In Taiwan, all medical institutions are required to provide a rightful indoor environment which meets the new Indoor Air Quality (IAQ) standards. Adding ventilation with fresh air is the major issue in saving energy, while medical institutions simply try to provide a healthy environment for patients and staff. The objective of this study was to assess an IAQ automatic ventilation management system in providing a healthy indoor environment while saving energy. Methods: In this study, the indoor ppm of carbon dioxide (CO₂) and the number of people were taken as primary variables for monitoring IAQ. Rolling calculations of population, quality of outdoor air and amount of indoor CO₂ were used to control the air conditioning system to supply the proper amount of fresh air. The new automatic ventilation management system effectively met the legal standard, provided a healthy indoor environment, and lowered energy consumption. Results: Through long-term monitoring and operation, the automatic ventilation management system reduced the concentration of CO₂from a peak value of 1400ppm to 900ppm, a decrease of 600ppm. Conclusions: The automatic ventilation management system has operated for two years, and improved the environment IAQ by 40%.