As an efficient and typical radiation source, heavy ion beam was widely used in biological mutagenesis breeding. The heavy ion beams of different mass, different charge number and different energy have their special processes and effects when interacting with the biological cells, which underwent physical, chemical and biological three stages, and led to end point biological effects ultimately, such as low doses of radiation sensitive phenomena and active oxygen metabolism changes. This article focuses on the primary endpoint of biological effect about the micro-organisms after the heavy ion beam irradiation, and the achievements made by heavy ion irradiation for microbial mutation breeding in agriculture and industry field in recent years.Cited