In the symbiotic region of Haloxylon ammodendron and Syntrichia caninervisin Gurbantunggut Desert, the bare patches of moss crust are often formed under H. ammodendron canopy. In order to study the mechanism of bare patch formation, the soil in the bare patch, the soil under the moss crust outside the bare patch, the bare ground soil of background, and the soil under the moss crust of background were used as research objects. The nutrient contents and physicochemical properties of four types of soil were measured, the soil metabolome was determined, and the differences between these soil indicators were analyzed. The results showed that there were no significant difference in nutrient content and ecological stoichiometry among the soils in the bare patches, the soil under the moss crust outside the bare patch, and the soil under the moss crust of background. Soil nutrients and ecological stoichiometry were not the cause of moss bare patches formation under H. ammodendron canopy. The contents of Na⁺, K⁺, Mg²⁺, SO^2-₄, CO^2-₃ and HCO^-₃ in the bare patch soil were significantly higher than those in the soil under the moss crust outside the bare patch, the bare ground soil of background, and the soil under the moss crust of background, with the highest total salt content being 1.705 g/kg. This salt content was not enough to affect the normal growth of the S. caninervis, so the higher ion concentration in the bare patch soil were also not the reason for moss bare patches formation. The soil metabolome results showed that there were significant differences in the metabolites of different soils, and amide compound such as oleamide had the highest relative abundance accounting for 72.68% of the total metabolites. The relative abundance of amide compound in the bare patch soil was significantly higher than that in the soil under the moss crust outside the bare patch, the bare ground soil of background, and the soil under the moss crust of background. Therefore, it is speculated that the amide compound such as oleamidein the bare patch soil may be the main reason for inhibiting the growth of S. caninervis, and are the main soil mechanism for moss bare patches formation under H. ammodendron canopy in Gurbantunggut Desert.