The interaction between low-energy ions and matter has been concerned rarely comparing to that of high-energy ions. It is even more unusual to find studies of the interaction of low-energy ions and complicated organisms. However, the discovery of bioeffects induced by ion beam implantation has opened a new branch in the field of ion beam applications in the life science—Low-energy heavy ion biology. The mutagenic effect of low energy heavy ions was firstly reported in 1986 in rice. Since then, a damage mechanism involved in energy absorption, mass deposition, and charge exchange has been proposed. Accumulating evidence has indicated that these three factors are key determinants in the bioeffects induced by low energy heavy ions, which has opened new opportunities for mutational breeding, gene transferring, cell modification, and cell fusion. In recent years, the ion beam implantation technique has been widely applied in many fields, and increasing research interest in the field has been seen. In this paper, we summarize recent advances in research on the role of low-energy ions interms of the mechanisms and applications.