Salinity is a major abiotic stress in arid and semiarid areas that has major effects on plant growth, thereby significantly reducing productivity. Biological soil crusts stabilize soil surfaces and aid in the establishment of vascular plants. These crusts have evolved salt resistance mechanisms and unique structures for survival under salinity stress and thus are an integral part of the soil system in arid regions worldwide. However, the effects of salinity on the ultrastructure of biological crusts have not been well investigated. Syntrichia caninervis Mitt is the dominant species in moss crusts of the Gurbantunggut Desert of northwestern China. In this study, S. caninervis was cultured in a concentration gradient of NaCl solution (0, 100, 200, 300, 400, 500 mmol/L) for 7 days. Using transmission electron microscopy, we observed changes in S. caninervis leaf cellular ultrastructure in response to salt stress. Comparisons of changes in cell wells, chloroplasts, and nuclei under the NaCl concentrations showed that under normal conditions (0 mmol/L NaCl), mesophyll cells were arranged loosely, organelles were morphologically integrated, and starch grains and electron-dense globules (plastoglobuli) were present in chloroplasts. No changes in ultrastructure were observed under mild NaCl stress (0-100 mmol/L); the cell structure was intact, and there were no changes in the structure of stroma or mitochondria. Under moderate NaCl stress (200-300 mmol/L), large changes in S. caninervis mesophyll cell structure were found, including swelling of the chloroplast thylakoid membranes, disorganization of grana, and plasmolysis. In addition, there was a marked increase in the number of plastoglobuli, the large central vacuole was ruptured, and chloroplasts showed disintegration. Overall, the ultrastructures of cell nuclei and vacuoles were slightly degraded. Under severe NaCl stress (400-500 mmol/L), the chloroplast membranes and lamellar structures were disorganized and contained a mass of plastoglobuli, and mesophyll cells were degraded and contained many vesicular multicycle-like membrane structures. Cells of the crust moss appeared to have serious plasmolysis as evidenced by the complete collapse of chloroplasts. These results indicate that injury to the membrane structure of various organelles, especially chloroplasts, is associated with the eventual death of mesophyll cells. Therefore, a better understanding of salinity-induced structural variability in Syntrichia caninervis should facilitate the identification of salt-tolerance mechanisms.