Arbuscular mycorrhizal fungi (AMF) can significantly influence the soil carbon cycle, however, their impacts on desert soils are still unclear. Here, a field control experiment, using in‐growth mesocosms, was conducted to quantitatively assess the contribution of AMF and ephemeral plants to ecosystem respiration (Re) and methane (CH4) flux in the Gurbantunggut Desert in China, from April to May 2017. Ephemeral plant biomass was significantly increased by AMF infection. Re was significantly positively correlated with AMF infection rate, whereas CH4 flux was significantly negatively correlated. The contribution of AMF to Re was up to 24%, comparable to the contribution of non‐AMF microbial respiration, which accounted for up to 36%, whereas the respiration of ephemeral plants accounted for 40%. Variation in Re was most strongly associated with soil organic carbon and soil available potassium concentrations and soil temperature. Non‐AMF microorganisms accounted for most of the CH4 flux (up to 85%). In contrast, AMF only accounted for 15% of total CH4 flux. The CH4 flux was significantly influenced by soil NO3−‐N content, soil moisture, soil temperature and soil NH4+‐N content. Overall, AMF significantly influenced Re and CH4 flux, and also enhanced the growth of ephemeral plants, which have an important role in the carbon cycle in desert ecosystems.