Recent researches on plant factory system deal with the convergence of lighting technology, agricultural technology inclusive to the high-tech industries worldwide in order to respond to the decreasing crop harvest due to global warming and abnormal weather phenomena. However, the fundamental performance standard is not currently being introduced in the case of plants factory and its commercialization is not activated because of high initial investment and operating cost. Large portion of the initial investment and operating cost of a plant factory is ascribed to artificial light sources and thermal control facilities, therefore, innovation should be provided in order to improve the economics of the plant factory. As an alternative, new plant factory could harness solar thermal and geothermal systems for heating, cooling and ventilation. In this study, a natural light dependent multi-layer plant factory’s thermal environment was analyzed with two-dimensional numerical methods to elicit efficient operation conditions for optimized internal physical environment. Depending on the supply air temperature and airflow rate introduced in the facility, the temperature changes around the crops was interpreted. Since the air supplied into the plant factory does not stay long enough, the ambient temperature predicted around the plating trays was not significantly different from that of the supplied air. However, the changes of airflow rate and air flow pattern could cause difference to the temperature around the planting trays. Increasing the amount of time of air staying around the planting trays could improve energy performance in case the thermal environment of a natural light based multi-layer plant factory is considered.