The total anthocyanin (TAC) and total isoflavone (TIC) contents were in the ranges of 189.461–2633.454 mg/100 g and 2.110–5.777 mg/g, respectively and were significantly different among the black soybean varieties. The contents of six anthocyanins, twelve isoflavones, and total phenolic, and the antioxidant activities were determined, and the association of each with seed weight was analyzed. In this study, seeds of 24 black soybean varieties and a reference genotype were grown in Korea, and grouped as small ( 24 g) seeds based on their seed weight. Due to these, seed weight is receiving much attention in soybean breeding. Seed weight is regulated by several genes which in turn could affect the metabolite contents, yield, and quality of soybean seeds.