Abstract: To study the biological effects of ¹²C⁶⁺ ion beams on dry seeds of Artemisia annua L, there are four indicators:survival rate, root length, hypocotyls length, plant height. The results showed that survival rate and root length decreased with increasing doses. While the hypocotyl length first increased and then decreased, the plant height showed a trend of overall decrease, but the plant height increased and decreased at 60 and 90 Gy. After studying the application of M1 generation after irradiation of artemisinin SRAP(sequence related amplified polymorphism) technique, the results showed that the differences between control group and treatment group are embodied at the change of specific bands. All the results indicated that M1 seedings of Artemisia annua L. irradiated by ¹²C⁶⁺ ion has obvious biological effects on both the plant developments and genomic DNA variations.