Abstract: To study the allelopathic autotoxicity of residues in the process of harvesting Panax notoginseng, the changes in soil saponins in pot experiments were examined by adding the different concentrations of root residues. The ultrastructures of the roots in the hydroponic experiment were observed. Results showed that the content of total saponins in soil declined and species increased with increasing time. In the hydroponic experiment, with the increase in time and concentration, the cell walls of Panax notoginseng roots thickened and cell mycelia appeared. In addition, the cells began to shrink or even break, and no complete organelles emerged in the cell structure. Results suggested that the chemical substances produced by decomposing fibrils may be another factor that causes the allelopathic autotoxicity of Panax notoginseng.