In the present study, a 3-year pot experiment was conducted to investigate the agronomic performance of different generation hybrids between genetically modified (GM) soybean and wild soybeans as well as inheritance of the CP4-EPSPS transgene and its effects on the seed germination rate, aboveground biomass, and fecundity in F1, F2 and F3 populations. Furthermore, the expression of transgenic proteins in various hybrids was also investigated. The results showed that the F1 hybrids had higher germination rates (weaker dormancy) and lower pod and seed numbers than the wild soybean. The F2 and F3 populations also had higher germination rates than wild soybean, but the F2 and F3 populations had nearly the same biomass, pod and seed yield as their maternal parents across the whole life cycle; while the seed germination rate, biomass, and fecundity were similar in EPSPS negative, homozygous and heterozygous plants of F2 and F3 populations. Furthermore, EPSPS proteins were detectable in F1, F2 and F3 progeny at different growth stages. While EPSPS genes had little effect on crop growth and reproduction, hybridization between GM soybean to wild soybean may have more impact on hybrid growth and fecundity, especially the seed germination rate and fecundity. F1, F2 and F3 had lower seed germination but higher pod and seed production than GM soybeans, and these parameters were close to those of wild soybean. Such characteristics acquired by gene flow have the potential to promote the adaptability of hybrids and may increase the possibility of dispersal of transgenes through seed systems.