Soybean sprouts have good digestibility, high isoflavone content compared with soybean seeds, and large amounts of aspartic acid, which is effective in eliminating hangovers. However, the region between the cotyledon and hypocotyl in soybean sprouts appears purple, the product value of soybean sprouts reduces. To date, the scientific correlation among factors such as growth temperature, spray water temperature, and cultivation periods for soybean varieties related to purple color expression between the cotyledon and hypocotyl of soybean sprouts are unknown. The purpose of this study was to identify the factors regulating the expression of purple color between the cotyledon and hypocotyl of soybean sprouts. Of 15 Korean soybean varieties with purple color in the hypocotyls and flowers, 9 varieties, including Sowonkong, Wonhwang, Sinhwa, Eunhakong, Pungsannamulkong, Paldonamulkong, Kwangankong, Shingang, and Jangki showed purple color between the cotyledon and hypocotyl of sprouts. However, the remaining six cultivars, including Dachae, Myeongjunamulkong, Sobaeknamulkong, Sojinnamulkong, Anpyeong, and Jonam, did not show purple color. The proportion of soybean sprouts with purple hypocotyls was the lowest at $26^{\circ}C$ and there was no significant difference at the other three cultivation temperature conditions ($17^{\circ}C$, $20^{\circ}C$, and $23^{\circ}C$). Similar to the results of the cultivation temperature experiment at five different spray water temperatures ($10^{\circ}C$, $17^{\circ}C$, $20^{\circ}C$, $23^{\circ}C$, and $26^{\circ}C$), the proportion of soybean sprouts with purple hypocotyls was the highest at the lowest spray water temperature ($10^{\circ}C$), and lowest at the highest temperature. Additionally, there was no purple color expression in soybean sprout hypocotyls on the $3^{rd}$ day after soybean sprouting. However, the highest expression level was observed on the $4^{th}$ day. Then, on the $5^{th}$ day, the proportion of soybean sprouts with purple hypocotyls reduced significantly, compared with that on the $4^{th}$ day. The results showed that interaction among these factors under cultivation conditions was remarkably effective for the expression of purple color in hypocotyls under the dark condition. These results suggested that cultivation temperature and spray water temperature for purple color expression in soybean sprout hypocotyls are the most important factors in the sprout cultivation environment.