Abstract: To invesitgate the effects of clipping on seedling quality and physiocological characterstics after transplanting of flue-cured tobacco, Huayan 06 was used as the test material, the agronomic charactere and physiological metabolism indices after transplanting under different clipping times were measured. The result showed that more clipping times restrained significantly plant height, increased fresh and dry weight of biomass below ground level and reduced the water content of tobacco seedling, and increase chlorophyll content and activity of nitrate reductase significantly, soluble protein contents but not significantly. Total root absorbing area, root active absorbing area and volume of roots were the best with 3 clippings.