Abstract: Autotoxicity is one of the main problems in the continuous cropping of Lanzhou lily. The aim of this study was to determine the mechanism of the autotoxic effect of Lanzhou lily and identify the organic compounds responsible for its autotoxicity. Water extracts of the root and bulb were applied to young lily plants at different concentrations (10, 50, 100, and 150 mg/mL) to test their effects on early development. Spectrophotometry and titration methods were used to measure various physiological indexes in the seedlings, and gas chromatography-mass spectrometry was used to identify compounds in the extracts. The extracts inhibited seedling growth in a concentration-dependent manner. As the concentrations of the extracts increased, the activities of superoxide dismutase, peroxidase, and catalase first increased and then decreased, and the malondialdehyde content and relative conductivity decreased. The contents of proline and soluble sugars increased significantly when the extracts were applied at concentrations greater than 100 mg/mL. Twenty-three and 14 compounds were identified in chloroform extracts of the root and bulb, respectively, including indane, naphthalene, 2,4-bis(1,1-dimethylethyl)-phenol, 2-methoxy-4-vinylphenol, vanillin, dodecanoic acid, 4-hydroxy-3, 5-dimethoxy-benzaldehyde, tetradecanoic acid, phenyl isocyanate, 1, 4-benzenedicarboxylic acid, and bis(2-ethylhexyl) ester. Most of the identified substances are known to be allelopathic. These results showed that water extracts of the root and bulb of Lanzhou lily showed autotoxic effects on lily seedling growth.