Heterosis utilization is one of the effective means to raise the crop yield. With the rise of the third generation of "intelligent sterility hybrid breeding technology", nuclear sterility gene has been widely used in crop cross breeding. In soybean, ms6 as an important gene of nuclear sterility has been widely used in recurrent selection breeding, but it is rarely reported in hybridization breeding. In this study, 12 dCAPS markers were developed using SNP mutation site of soybean ms6 gene. Three dCAPS markers ms6-dCAPS-1, ms6-CAPS-2 and ms6-CAPS-3 were identified by restriction endonuclease digestion. Further verification showed that the ms6-dCAPS-3 marker was stable and reproducible. After restriction endonuclease Hind III digestion, the amplified products could accurately distinguish homozygous fertile, heterozygous fertile and homozygous sterile single strains in the isolated population of ms6 offspring. This provides an effective technical support for the application of nuclear sterile gene ms6 in hybrid soybean breeding.