Anthocyanins from the black soybean seed coat are known to have many pharmaceutical effects. However, black soybean seed contains antinutritional factors such as lipoxygenase, Kunitz trypsin inhibitor (KTI), lectin, and stachyose. The genetic removal of these components will improve the nutritional value of black soybean seed. The objective of this research was to breed a soybean strain with the black seed coat color, green cotyledon color, and tetra recessive allele (lox1lox2lox3/lox1lox2lox3-ti/ti-le/le-rs2/rs2) for lipoxygenase, KTI, lectin, and stachyose components. Eight parents were used to breed the tetra null strain. Analysis of lipoxygenase, KTI, lectin, and stachyose components in mature seeds was conducted by SDS-PAGE, Western blot, and HPLC. The soybean line with the black seed coat color, the green cotyledon color, a large seed size, and tetra recessive alleles has purple flowers, a determinate growth habit, and brown pods at maturity. The stem height of the breeding line was 52.3 cm. The 100-seed weight of the breeding line was 35.2 g and the yield (Ton/ha) was 2.50. The stachyose content of the breeding line was 3.30 g/kg. This is the first soybean strain with the black seed coat color, the green cotyledon color, a large seed size, and tetra null alleles (lox1lox2lox3/lox1lox2lox3-ti/ti-le/le-rs2/rs2, low content of stachyose, free of lipoxygenase, KTI, and lectin proteins).