With the development of biological technology, the study on biological effects induced by heavy ion beam irradiation is undergoing the transition from phenotype to genotype,  qualitation to quantitation both on the research methods and research objects, and gradually into the molecular level. At the molecular level, the living matter have specific behaviors of damage and repair when irradiated by heavy ion beam, this biological effects could be quantified by the related mathematical models, meanwhile, the studies of bystander effects induced by heavy ion beam irradiation are important to decrease the damage of healthy tissue in heavy ion radiotherapy.Cited