To reduce the energy consumption in buildings, modern buildings are increasingly becoming airtight. In these structures, the outdoor air is supplied inside through mechanical ventilation systems, which are essential for ensuring comfortable indoor air quality. However, these systems consume a considerable amount of energy in buildings. One potential solution is using a thermal labyrinth system, which is buried underneath the building. It can pre-cool or pre-heat the outdoor air through heat transfer with the surrounding soil. In this research, a number of case studies were conducted to optimize the thermal labyrinth design. The optimized thermal labyrinth system was derived using computational fluid dynamics (CFD) simulation. In addition, operation algorithms were developed for the efficient operation of the thermal labyrinth system in buildings. The results indicated that there were five operation modes, and the thermal labyrinth could be operated for seven months of the year. The energy reduction effects of the thermal labyrinth system were analyzed and were assessed by the transient system simulation (TRNSYS) tool. A 12% reduction in the annual heating and cooling energy was achieved by applying the thermal labyrinth system.