Glycine max cultivars Lee68, Nannong1138-2, Nannong8831 were used as the female parents, and hybrid lines (F 5) 4111, 4076 [N23674 × BB52], 3060 [Lee68 × N23227] and 185 [Jackson × BB52] that selected for salt tolerance generation by generation from the cross combination of G. max and G. soja were used as the male parents, 11 (A-K) backcrosses or three-way crosses were designed and 213 single hybrids were harvested. The optimized soybean SSR-PCR system was used to analyze the SSR polymorphism of above parental lines and get the parental co-dominant SSR markers for hybrid identification, and in which 30 true hybrids were gained. The true hybrids (G1, G3, G9, G12, G13, G16) of G cross combination were chosen as the representative for the salt tolerance test, and the results showed that, as exposed to salt stress, the seedlings of G9 line displayed higher salt tolerant coefficient, relative growth rate and dry matter accumulation, when compared with their female parent Nannong1138-2, and even performed equally strong salt tolerance as the male parent 3060. It provides a feasible method of the combination of molecular SSR markers and simple physiological parameters to identify the true hybrids of G. max and G. soja, and to innovate the salt-tolerant soybean germplasms.