As the highest stage in the development of biological soil crusts and the most important contributor of biomass to biological soil crusts, moss crust plays an important role in stabilizing the desert surface and improving the moisture and nutrient conditions of the micro-environment. Mosses are poikilohydric and are sensitive to pulsed precipitation and drought. Non-structural carbohydrates (NSC) are the important part of plants and can withstand the damage caused by environmental stress to plants. However, the response mechanism of non-structural carbohydrate to drought is not clear. In the present study, we chose Syntrichia caninervis, the dominant species of moss crusts in the Gurbantunggut desert, as the target species and examined the change in NSC content during the period of dehydration. The results showed that the water content decreased with the duration of dehydration, declining rapidly during 1-24 h, and then declining slowly. The change in NSC content is complicated. Soluble total sugar content (TSC), fructose content (FC), sucrose content (SUC), and starch content (STC) decreased rapidly in the first hour. The NSC, TSC, FC, SUC, and STC did not change significantly in the stem and leaves of plants during the second hour to sixteenth hour. The NSC, TSC, FC, SUC, and STC increased significantly during the sixteenth hour to twenty-fourth hour. From twenty-fourth hour to forty-eighth hour, the NSC, TSC, FC, SUC, and STC of moss in the central region of the desert decreased slowly and reached the level of incipient dehydration, and the TSC, FC, and SUC of the moss in the southern region of the desert significantly decreased. However, the NSC of moss present in the central region of the desert was not significantly different. This result indicated that the plant water content and NSC of moss from different regions show different changes in the process of rehydration and dehydration. The NSC of S. caninervis was differed significantly among regions. This study contributes to the understanding of the process by which non-vascular plants respond to pulsed precipitation and drought stress in desert.