The effects of difference length microwave radiation lsatis indigotica on germination ratio, activity of amylase, activity of ALT, activity of AST, activity of proteases, concentration of soluble protein, free amino acid concentration, DNA concentration, cotyledon area and biophoton emission were studied by using the seeds being irradiated with microwave after soaked for 3h. The results show that microwave radiation treatments with different time can improve the germination ratio, activity of amylase, activity of ALT, activity of AST, activity of proteases, concentration of soluble protein, free amino acid concentration, DNA concentration, cotyledon area and biophoton emission. And the microwave radiation of low doses can stimulate the seeds germination and improve the cotyledon development. The effect of 8s pretreatment of microwave therein mentioned is the best for lsatis indigotica fort.