In this study,the wide type seeds of Isatis indigotica were used as research materials,and carbon ions (irradiation doses:30Gy,60Gy,90Gy and 120Gy) were used to irradiate the seeds.The impact of different irradiation dosages on seed germination,seeding growth,main effective ingredients,genome and total protein polymorphism of I.indigotica were also comprehensively evaluated,which can provide a reference for I.indigotica breeding,molecular biology researching and the application of heavy ion irradiation mutagenesis.The results showed that:(1)the seedling surviving rate and root fresh weight of I.indigotica gradually decreased with enhanced irradiation intensity.Compared to other dosages,30Gy exhibited the minimum inhibition of growth and maximum increase of main effective ingredients 4(3H) quinoxalinol and indirubin in roots,by 2.2 and 2.3 fold compared to wide type,respectively.(2)SRAP analysis results indicated that the degree of genome variation was increased with enhanced irradiation intensity.Compared to wide type,mutants after using 30Gy had recovered 33.59% polymorphic variations for DNA.(3)SDS-PAGE gels stained by CBB and Pro-Q showed that total protein and phosphoprotein had been changed,but they were not positively correlated with the irradiation intensity,which indicates that plants may have a compensatory mechanism for the damage caused by heavy ion irradiation.After all,for I.indigotica mutagenesis,30Gy is the best carbon ion irradiation dosage which can induce a high content of active ingredients,and these results also laid a basis for mutation breeding of high quality I.indigotica.