To reduce the harm to raw water pipes by Limnoperna fortunei, the experimental study of inactivation effect on Limnoperna fortunei with potassium permanganate under different conditions in the raw water was conducted. At the same temperature, the inactivation effect increased with the concentration of potassium first; when the concentration reached 15 mg／L, the effect was the best; the inactivation effect was worse when the concentration was 18 mg／L. When the concentration was higher than 2 mg／L, the Limnoperna fortunei closed shells to protect themselves for a long time, 8 days or more. At this time, the mortality has little to do with the concentration. The results show that the concentration of potassium permanganate of 12-18 mg／L could achieve the purpose of killing Limnoperna fortunei as soon as possible with low costs. As the temperature increases, the killing effect is improved. The tolerance of Limnoperna fortunei of which the shell length is less than 10 mm or larger than 20 mm is weaker than that of others.