The effects of the deficiency of the allergenic α-subunit on soybean amino acid (AA) composition were studied using the cultivar Dongnong 47 (DN47) as a genetic background. The near-isogenic line (NIL) NIL-DN47-Δα of DN47, with an introgression of the α-null trait allele from the high protein donor parent RiB, was created by marker assisted background selection and used to investigate the AA content and nutritional quality. The contents of crude protein, the total AAs, the total essential amino acids (EAAs) and sulfur-containing (Met and Cys) AAs increased by 4.11％, 4.16％, 5.20％ and 11.96％, respectively in NIL-DN47-Δα compared with DN47. Analyses of the total EAAs (TEAAs) and the EAA index (EAAI) revealed that both parameters in NIL-DN47-Δα were higher than those in DN47. The null-allele of the α-subunit positively affected the AA scores. The quantitative changes in free AAs (FAAs) in the developing seeds of NIL-DN47-Δα and DN47 were compared as of 15 days after flowering (DAF) until maturity. The results showed that the total FAA content in NIL-DN47-Δα was significantly higher than that in the DN47 throughout the late maturation stage (40-60 DAF) of seeds. The high concentration of the FAAs in cgy-2 mutant seeds was a consequence of the high rates of synthesis and/or accumulation of individual FAAs during seed maturation where 25 DAF was an important turning point in the accumulation of the FAAs. The FAA contents of single soybean α-null, double (α+α′) and triple (α+α′+group I)-null mutant combination lines were investigated. In all of these combinations, introduction of the cgy-2 gene invariably raised the FAA content of mature seeds above that of the DN47. In summary, the enhanced protein quality in cgy-2 mutants resulted from several factors. (1) There was a general increase in the contents of most AAs and FAAs in NIL-DN47-Δα. (2) The induced synthesis of free Arg contributed effectively to the high FAAs of various storage-protein-deficiency mutants. For example, in the S2 (null α, group I), the free Arg content was seven times as much as that of DN47, accounting for more than half of the total FAA content in the seed. (3) The increase of sulfur-containing AAs in the α-null type NIL mainly resulted from elevated Met content. These data suggested that the cgy-2 mutation might improve the protein quality of soybean seeds and that lacked of the allergenic α-subunit resulted in increased the FAA content.