In this study soybean cultivar Zhong Huang 18 was used as materials, and the genetic integrity of population with different germination percentage and their descendant population was investigated by 60 core SSR primers. The result showed that there was no significant difference in the allelic frequencies and the effective number of alleles of the aged population and their descendant population compared with the control population. It indicated that the allelic frequencies of the aged population and their descendant population changed slightly. There was no significant difference in the number of alleles, the index of genetic diversity, Shannon’s information index and the number of rare alleles between the control population with the germination percentage of 98% and its first and second descendant population, and the value of genetic identity was relatively high. The number of alleles, the index of genetic diversity, Shannon’s information index and the number of rare alleles of the aged population (G0-3 and G0-4) with the germination percentage below 85% and their first and second descendant population were significantly reduced compared with the control, and the value of genetic identity was relatively high.Therefore, seed aging maybe had a greater impact on the genetic composition of the soybean population than regeneration times.