We analyzed greenhouse gas fluxes at the different growth stages of algae and lichen crusts in fixed sand with mobile dune as control in the eastern Hobq Desert, China, using the spatio-temporal substitution method. We explored the correlation of these fluxes with environmental factors and with biological soil crust growth. The results showed that variation of CO2 fluxes followed the order: lichen crust (128.5 mg·m-2·h-1) > algae crust (70.2 mg·m-2·h-1) > mobile dune (48.2 mg·m-2·h-1). CH4 absorption rates were in the following order: lichen crust (30.4 μg·m-2·h-1) > algae crust (21.2 μg·m-2·h-1) > mobile dune (18.2 μg·m-2·h-1). The N2O fluxes were in the following order: lichen crust (6.6 μg·m-2·h-1) > algae crust (5.4 μg·m-2·h-1) > mobile dune (2.5 μg·m-2·h-1). CO2 emission had obvious seasonal variation, with higher emission in the growing season. CH4 and N2O fluxes had no seaonal variation. CH4 absorption mainly occurred in the growing season and N2O emission mainly occurred in non-growing season. Contents of soil total nitrogen and organic carbon and the abundance of microorganisms were important factors affecting greenhouse gas fluxes. Hydrothermic factors were important for soil CO2 emission, but not for CH4 and N2O fluxes. The cumulative greenhouse gas emissions were gradually increased with vegetation restoration and the development of biological soil crust. The global warming potential increased following an order: lichen crust (1135.7 g CO2-e·m-2·a-1) > algae crust (626.5 g CO2-e·m-2·a-1) > mobile dune (422.7 g CO2-e·m-2·a-1). biological soil crust, desert ecosystem, global warming potential, greenhouse gas, vegetation restoration