Abstract: To explore the effects of high-energy heavy ion beams irradiation on the physiological and growth characteristics of Scutellaria baicalensis Georgi seedlings, different doses of carbon ion beam with total energy of 967 MeV were selected to irradiate seedlings to measure the survival rate, seedling height, number of leaves, number of branches, biomass, root-shoot ratio, antioxidant enzyme activity, photosynthetic characteristics and content of secondary metabolites. The results showed that the semi-lethal dose of seedlings was 32.82 Gy. The seedling height, number of leaves, number of branches, and biomass of Scutellaria baicalensis increased under 5 and 10 Gy, but decreased under 30 Gy compared with the control group. The activities of superoxide dismutase (SOD) and peroxidase (POD) in all treatment groups increased to reduce the damage of reactive oxygen species caused by irradiation. The content of chlorophyll in leaves decreased with the dose within 6 weeks after irradiation; the content of total chlorophyll, net photosynthetic rate and stomatal conductance of leaves increased under 5 and 10 Gy in 9 weeks after irradiation. In addition, the accumulation of total flavonoids and baicalein in the root were promoted under 10 Gy. These results indicated that 10 Gy heavy ion beams not only stimulated the growth, but also increased the content of medicinal ingredients in Scutellaria baicalensis. The study explored the contemporary biological effects of heavy ion beams radiation on Scutellaria baicalensis Georgi, which provides a basis for the follow-up research on irradiation stimulation effects and radiation breeding of Scutellaria baicalensis Georgi.