Abstract: This paper introduced an effect capillary zone electrophoresis method for screening of stevia mutation. According to the experimental results, the optimum separation conditions were selected as: 60 mmol/L Tristetraborate buffer of pH 8.0, 30 ℃ and 25 KV. Under optimum conditions, the R.S.D. of stevioside migration time for 15 runs was 0.45%. The detector response for stevioside was linear over the range of 7.45×10-5～1.74×10-2 mol/L (r=0.9994). Stevia main sweeteners cound be separated effectively in less than five minutes. This method was applied for determining the variation of stevia main sweeteners after low_energy ions implantation.