Ion beam bio-engineering was established by Chinese researcher in 1980s. Over thirty years past, there were delightful progress by low energy ion beam induced mutants and crop improvement. When ion beam implant the organism, charge exchanged between ions and organism surfaces. Meanwhile there were ion sputtering, ion penetration and surface damage of plant cell wall material. Owing to etching action of low energy beam to plant cell wall, ion beam mediated exogenous DNA transformation becomes possible. Representative applications and achievements in crop breeding were described.