Desert mosses, which are important stabilizers in desert ecosystems, are distributed patchily under and between shrubs. Mosses differ from vascular plants in the ways they take up nutrients. Clarifying their distribution with ecological stoichiometry may be useful in explaining their mechanisms of living in different microhabitats. In this study, Syntrichia caninervis, the dominant moss species of moss crusts in the Gurbantunggut Desert, China, was selected to examine the study of stoichiometric characteristics in three microhabitats (under living shrubs, under dead shrubs and in exposed ground). The stoichiometry and enzyme activity of rhizosphere soil were analyzed. The plant function in the above-ground and below-ground parts of S. caninervis is significantly different, so the stoichiometry of the above-ground and below-ground parts might also be different. Results showed that carbon (C), nitrogen (N) and phosphorus (P) contents in the below-ground parts of S. caninervis were significantly lower than those in the above-ground parts. The highest N and P contents of the two parts were found under living shrubs and the lowest under dead shrubs. The C contents of the two parts did not differ significantly among the three microhabitats. In contrast, the ratios of C:N and C:P in the below-ground parts were higher than those in the above-ground parts in all microhabitats, with significant differences in the microhabitats of exposed ground and under living shrubs. There was an increasing trend in soil organic carbon (SOC), soil total nitrogen (STN), soil available phosphorous (SAP), and C:P and N:P ratios from exposed ground to under living shrubs and to under dead shrubs. No significant differences were found in soil total phosphorous (STP) and soil available nitrogen (SAN), or in ratios of C:N and SAN:SAP. Higher soil urease (SUE) and soil nitrate reductase (SNR) activities were found in soil under dead shrubs, while higher soil sucrase (STC) and soil β-glucosidase (SBG) activities were respectively found in exposed ground and under living shrubs. Soil alkaline phosphatase (AKP) activity reached its lowest value under dead shrubs, and there was no significant difference between the microhabitats of exposed ground and under living shrubs. Results indicated that the photosynthesis-related C of S. caninervis remained stable under the three microhabitats while N and P were mediated by the microhabitats. The growth strategy of S. caninervis varied in different microhabitats because of the different energy cycles and nutrient balances. The changes of stoichiometry in soil were not mirrored in the moss. We conclude that microhabitat could change the growth strategy of moss and nutrients cycling of moss patches.