[Objective] The aim was to explore the biological effect of low energy ion beam mediated parameters with fractional factorial design method. [Method] The twin-embryos seed of autotetraploid rice DER10-04-01 was taken as the receptor material,and the Elymus dahuricus Turcz. was used as materials to provide DNA to carry out the ion beam mediated experiment. And the fractional factorial design method was used to study the parameters of low enery N+ ion beam mediated foreign genes into rice. [Result] The implantation energy,dose,DNA concentrations and immersion time of DNA showed significant biological effects on the normal growth and development of DER10-04-01,in which the biological effects of implantation dose and DNA concentrations were relatively obvious. [Conclusion] The implantation energy,dose,DNA concentrations and immersion time of DNA were major factors showing important effects on the experimental result in ion beam mediated foreign genetic materials.