Changes in temperature and precipitation are expected to influence the function of desert ecosystems by altering the biogeochemical cycles of elements. Biocrusts can introduce additional nitrogen (N) and carbon (C) to arid ecosystems through N fixation and photosynthesis. Although biocrusts are the main N contributor in desert ecosystems, it remains unclear how the nitrogenase activity (NA) of biocrusts responds to the prolonged warming coupled with precipitation reduction that is predicted to occur with climate change. To address this important knowledge gap, the experiment including two groups of open-top chambers was designed to simulate the predicted climate change in an arid desert. In a simulation experiment conducted over 14 years, the NAs of cyanobacteria- and moss-dominated crusts were determined by acetylene reduction assay. In parallel, the water increment, NO3–-N, NH4+-N, total N content, and absolute abundance of nifH-gene were also determined. The results showed that in cyanobacteria-dominated crusts, 0.5 °C-warming coupled with a reduction in precipitation (abbreviated as 0.5 W-RP) increased the NA, while 1.5 °C-warming coupled with a reduction in precipitation (1.5 W-RP) decreased the NA and the biocrust-soil total N content. The abundance of nifH-gene in the cyanobacteria-dominated crusts increased under the two warming scenarios. Both 0.5 W-RP and 1.5 W-RP promoted the NA in the moss-dominated crusts, simultaneously reducing the abundance of nifH-gene. However, there was no N pool increase in the cyanobacteria-dominated crusts with 1.5 W-RP and in the moss-dominated crusts under the two warming scenarios. In contrast, the results suggested that there may be an increase in nitrogen input in cyanobacteria-dominated crusts under lower warming.