The herbaceous plants are rare under the crown of the natural Populus euphratica stands (referred to as bare spots) in the arid Populus euphratica sparse forest area. To study the allelopathic formation mechanism of the bare spots under the Populus euphratica canopy, the soil inside and outside the bare spots and the litter under the canopy were used as the research objects in Ebinur Lake. We analyzed metabolomes of different samples using LC-MS technology, used PLS-DA to identify and screen metabolite differences in each group, and screened out significant differences in metabolites and their metabolic pathways in soil samples inside and outside of the bare spots. The results of the study showed that 908 total metabolites (615 positive and 293 negative) were identified in soil samples; a total of 1,291 total metabolites (760 positive and 531 negative) were identified in litter samples. By annotation and classification, it is found that the relatively quantitative values of allelochemicals such as Kojic acid, Microcystin, Theophylline, Suberic acid, Arachidonic acid and Trans-cinnamic acid were significantly higher in the bare spot than that in the soil under the tree canopy; In litter samples the relative quantitative values of allelochemicals such as Catechin, Caffeic acid, Indole, Palmitoleic acid, Cumin aldehyde, Ferulic acid, Trans-cinnamic acid, Arachidonic acid, Salicylic alcohol and Coumarin were significantly higher than that in soil samples. The accumulation of the above potential allelopathic substances in soil under Populus euphratica canopy and its litter may enhance the allelopathic effect of plants, leading to restrictions on the germination and growth of herb seeds under the Populus euphratica canopy.