The interest in phytochemicals from crops has grown in recent years, with soybean, as a functional crop, having great potential for providing a high level of nutrition. Therefore, the aim of this study was to evaluate phytochemicals from Korean soybean varieties, and to provide the basic information necessary for targeted breeding of soybean. The seeds of 172 soybean varieties were collected from various domestic institutes, and their phytochemicals were analyzed and compared based on agronomic characteristics (color, size, usage, etc.) using cluster analysis. We found that the soybean varieties contained relatively higher levels of the following phytochemicals: lutein (3 var., >7.0 μg g−1 seed), tocopherols (26 var., >300 μg g−1 seed), and phytosterols (33 var., >1000 μg g−1 seed). Overall, phytochemical levels were higher in varieties released since 2000 and with small-sized seeds (<12 g, 100-seed weight). The distribution of phytochemicals varied according to the usage (cooking, sauce, sprouts, etc.), even though the highest levels of each phytochemical were mainly observed in sprouts. The cluster analysis using three main components classified the varieties into five groups. Of them, group III showed relatively higher tocopherols, group IV had relatively higher lutein, and group I had relatively higher phytosterols. Jonam and Manpoong (group I) were observed in varieties high in phytochemicals. Overall, some Korean soybean varieties were found to have relatively higher levels of phytochemicals compared to those reported in previous studies of other origins. In conclusion, our findings suggest that some varieties might provide suitable breeding material for target-centered improvement of soybean varieties, and a comparison between different origins is necessary for providing better knowledge for soybean breeding.