Dwarfing is useful to reduce plant height, when breeding high-yielding and non-lodging crops. In this study, a set of natural storage protein subunit-null dwarf mutants of soybean was reported that showed strongly reduced plant stature and deficiency in various 7S and 11S subunits, designated as snd1 mutants. Under normal growth conditions, the snd1 mutants showed a severe dwarf phenotype, with plant height of about 25 cm. Compared with wild-type DN47, the mutant snd1 exhibited no obvious morphological differences at the early stage of development. All the snd1 mutants examined had fewer nodes and shorter than normal intodes;the leaves were similar in shape to normal parents, but were dark-green at the mature stage. The flower size was similar to DN47;however, the flowering period was shorter than in the wild-type. Significant variation was noted for protein content, oil content of the seeds and size of seeds (weight of 100 seeds) among 17 snd1 dwarf lines. Genetic analysis indicated that the dwarfism of snd1 was controlled by a single recessive gene. The snd1 dwarf mutant had markedly different dynamic levels of the endogenous hormones gibberellin (GA), brassinosteroid, indole-3-acetic acid and abscisic acid, at the seedling stage. Exogenous GA3 treatment led to recovery of the plant height phenotype of the snd1 mutant; GA3 at 0.1 mm had the largest effect on enhancing plant height. Using molecular markers, snd1 gene was approximately mapped in an interval of 603 kb between markers Satt166 and Satt561 on chromosome 19. Snd1 mutant provided valuable material for hypoallergenic soybean breeding and the snd1 gene might be a novel gene related to plant height in soybean.