Syntrichia caninervis is a typical drought-tolerant moss found worldwide in various semiarid and arid regions. Biological soil crusts (BSCs) develop well in Gurbantünggüt Desert, and S. caninervis is a dominant species in the moss crusts of this cold desert. Gurbantünggüt Desert is home to stable and abundant snow cover in winter, little rain in spring, and high temperatures and drought in summer. There is a large variation in climatic conditions across seasons in Gurbantünggüt Desert. The leaves of desert moss have only a single layer of cells, and thus are extremely sensitive to the changing environment. However, there have been few studies exploring how desert moss maintains its physiological functions even under such a drastically changeable environment. One of the major goals of this study was to investigate the physiological regulatory mechanisms and relevant antioxidant enzyme activities of S. caninervis in different microhabitats and seasons. Microclimate and soil conditions were continuously monitored in sampling sites starting in November 2013. We measured physiological and biochemical characteristics of S. caninervis, including water content; concentration of proline, soluble sugar, soluble protein, and malondialdehyde (MDA); and activity of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). The results showed that, in different seasons, microhabitats and their interactions significantly affected the content of proline, soluble sugar, soluble protein, and MDA in shoots of this species, as well as the enzyme activity of CAT, POD, and SOD. Extreme high temperature and drought caused significantly high proline and soluble sugar content and higher CAT, POD, and SOD activity, but soluble protein content was the lowest in summer among the three seasons. The aridity in spring caused significantly higher proline and soluble sugar content than in winter. Moreover, there was higher MDA content and CAT activity in low-temperature winter than in spring. According to correlation analysis, MDA content, and POD, CAT, and SOD activity all had significantly negative correlations with plant water content, whereas all the physiological and biochemical characteristics displayed no significant correlations with plant water content in winter. In spring, all the physiological and biochemical characteristics, except soluble sugar content, had significantly negative correlations with plant water content, whereas proline content and temperature had no significant correlations with the other physiological and biochemical characteristics. Furthermore, during the summer, all the physiological and biochemical characteristics had significantly negative correlations with plant water content and significantly positive correlations with temperature. These findings suggested that the desert moss experienced different types of stress in the three seasons:low-temperature stress in winter, drought stress in spring, and drought and high-temperature stresses in summer. When compared to those growing in other habitats, under shrubs and on open ground, because the snow cover decreased the effects of the shrubs, there was no difference in the characteristics that reflect physiological and biochemical activities between the two microhabitats in winter. Furthermore, shrubs could provide a moister environment for S. caninervis than exposed ground for the duration of desiccation (spring and summer). As a result, the osmoregulation substance contents and antioxidant enzyme activities in the mosses under the shrubs were lower than in those on exposed grounds. This may suggest that S. caninervis growing on exposed ground has a greater tolerance to stress in harsh environmental conditions than those occurring under live shrubs.