Abstract: Uncertainties still existed for evaluating greenhouse gases fluxes (GHGs), including carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) at the regional scale for desert ecosystem because available GHGs data about biological soil crusts (BSCs) was very scarce. In 2011 and 2012, soil ecosystem covered by various types of BSCs and BSCs at different succession stages in an artificial sandfixing vegetation region established in various periods at southeast of the Shapotou area in Tengger Desert was selected to measure fluxes of CO₂, CH₄ and N₂O using static chamber and gas chromatography. The results showed that curst type, recovery time and their interactions with sampling date significantly affected CO₂ flux. Recovery time and interaction of crust type and sampling date significantly affected CH₄ flux. Sampling date significantly affected the fluxes of CO₂, CH₄ and N₂O. The mean annual flux of CO₂ for moss crust (105.1 mg·m^-2·h^-1) was significantly higher than that of algae crust (37.7 mg·m^-2·h^-1) at the same succession stage. Annual mean CH₄ and N₂O consumption was 19.9 and 3.4 μg·m^-2·h^-1, respectively. Mean annual consumption of CH₄ and N₂O for algae crust was slightly higher than that of moss crust, however, significant difference was not found. Ecosystem respiration (Re) of desert soil covered by BSCs increased with the recovery process of desert ecosystem, in contrast, consumption of CH₄ and N₂O decreased. Re of moss crust was more sensitive to temperature and moisture variation than algae crust and Re sensitivity of temperature and moisture gradually increased with the development and succession of BSCs. Both soil temperature and moisture were not the main factor to determine CH₄ and N₂O fluxes of BSCssoil in desert ecosystem.