By taking 2.5% (w/w) transgenic Roundup Ready Soybean as raw materials, with the detecting technology of traditional PCR and real-time fluorescence quantitative PCR, this study analyzed the influence of such critical processing procedures as jordaning, siruping, blending, homogenization and sterilization in soymilk preparation on the fragment size of endogenous gene lectin and exogenous gene epsps, as well as the quantification of transgenic component in Roundup Ready Soybean, and discussed the degradation mechanism of DNA in the course of transgenic soybean processing. The results indicated that, different processing procedures differ in their impact on the degradation of endogenous gene and exogenous gene. Physical mechanical action, such as the jordaning, can make endogenous and exogenous genes degrade, and has more effect on the later. The jordaning process degraded the DNA of endogenous gene from 1883 to about 836 bp, and exogenous gene from 1512 bp to about 408 bp. In the blending procedure, exogenous gene DNA was also degraded from about 408 to 190 bp, but there was no obviously action on the endogenous gene. After the endogenous and the exogenous genes were degraded to some degree, such as 836 and 408 bp, respectively, they were not evidently affected by siruping procedure at 100 degrees C for 15 min. However, endogenous gene was further considerably degraded from around 836 to 162 bp in the sterilization procedure at 121 degrees C for 30 s. The effect of the homogenization step on endogenous and exogenous genes was similar to that of siruping procedure. In addition, jordaning and siruping greatly damaged to exogenous gene, which rapidly decreased the transgenic content from 2.5 to 1.656% and 0.435%, respectively. While the endogenous gene was not evidently affected by the blending and homogenization procedures, the exogenous gene DNA was remarkably degraded in the two procedures. Therefore, the transgenic content continued decreased to 0.377% after homogenization procedure. Hereafter, the endogenous gene was further considerably degraded more than the exogenous gene in the sterilization procedure, which caused a little bounce of the transgenic content in the final product to 0.518%.