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The autotoxicity of root exudates and the change of rhizosphere soil microbes are two important factors that affect the quality and yield of Lanzhou lily (Lilium davidii var. unicolor). Phthalic acid (PA) is a major autotoxin of the root exudates in Lanzhou lily. In this study, we treated plants with different concentrations of PA from the Lanzhou lily root exudates and then analyzed the effects of autotoxins on fresh weight, shoot height, root length, and Oxygen Radical Absorbance Capacity in root. The diversity of soil fungi in Lanzhou lily soil was analyzed using MiSeq. The results showed that PA induced oxidative stress and oxidative damage of Lanzhou lily roots, improved the level of the membrane lipid peroxidation, reduced the content of antioxidant defense enzyme activity and the nonenzymatic antioxidant, and eventually inhibited the growth of the Lanzhou lily. We found that continuous cropping of Lanzhou lily resulted in an increase in fungal pathogens, such as Fusarium oxysporum in the soil, and reduced the size of plant-beneficial bacteria populations. The results in this study indicate that continuous cropping would damage the regular growth of Lanzhou lily.