In the middle 1980s, Chinese researchers first studied the mutagenic effects of low energy ion beam, and successfully applied it to plant breeding. With the development of ion implantation technique, it will offer great prospect in cell fusion and genetic manipulation. Meanwhile, progresses have also been made on the mechanisms. In this paper after a brief review on the low energy ion-implanting device we will study the biological effects of plant that are induced by low energy ion beam implantation, with an emphasis on the mutation breeding of plant by the low energy ion beam and the gene transfer induced by it. Then we will discuss the interaction process of low energy ions and the mechanism of ion beam induced biological effects. In the last section, we will give a short comment on the prospect of low energy ion beam bioengineering.