Background: The growth process of ginseng seedlings is very important in producing good quality ginseng. This study was carried out to investigate the effects of different microclimates on the growth characteristics of ginseng seedlings in a multi-layer bed facility. Methods and Results: Ginseng seedlings were cultivated in a three-layer bed facility. The air temperatures on the first and second floors were similar, while that on the third floor was about 1 - 4℃ higher than that on the other floors. The vapor pressure deficit (VPD) was higher inside than on the outside of the facility, and that on third floor was the highest in the multi-layer bed system. The photosynthetic rate, chlorophyll fluorescence, and growth characteristics of ginseng seedlings did not significantly differ among the three floors. The yield of ginseng seedlings was the highest at 721 g/1.62 ㎡ on the first floor Conclusions: It was found that microclimate plays an important role in growing ginseng seedlings in multi-layer bed facilities, and therefore proper environmental control is important. In addition, producing ginseng seedlings using multi-layer bed facilities is a technology that is expected to provide a way to overcome climate change and stabilize ginseng production.