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Biocrusts are a crucial component of desert ecosystems, playing a significant role in greenhouse gas fluxes when they cover soils. However, little is known about whether, and how sand burial, one of the most common disturbances affecting the biodiversity and ecological function of biocrusts, influences fluxes of CO2, CH4, and N2O from the desert biocrust-covered soils. Based on measurements of the fluxes of three greenhouses gases from soils covered with two kinds of biocrusts separately dominated by mixed (i.e., approximately 50% algal coverage and 50% lichen coverage of Endocarpon pusillum Hedw., here cyanobacteria are classed as algae) and moss (i.e., 100% coverage of Didymodon vinealis (Brid.) Zand.) crusts respectively, followed by zero (control), 1 mm (shallow burial), and 10 mm (deep burial) burial depths of sand, we studied the effects of short (20 days) and relatively long periods (one year) of sand burial on the fluxes of three greenhouse gases as well as their relationships with soil temperature and moisture at Shapotou on the southeastern edge of the Tengger Desert. The results of this study showed that sand burial had a significantly positive effect on emission fluxes of CO2 and a negative effect on uptake of CH4 by soils covered with the two types of biocrusts (P < 0.05), but had a differential effect on N2O fluxes depending on burial depth. Shallow burial dramatically increased N2O emissions from the biocrust-covered soils (P < 0.05), but the opposite was observed under deep burial. As burial time increased, the increase of CO2 emissions decreased, but changes in fluxes of CH4 and N2O varied with biocrust types and burial depths, respectively. In addition, results showed that CO2 fluxes from the two biocrusts were closely related to soil temperature and moisture; thereby increased with the raised soil temperature at 5 cm depth and soil moisture caused by sand burial. In contrast, CH4 and N2O emissions were not clearly related to temperature or moisture. Overall, the increase in global warming potential caused by sand burial indicates that this kind of deposition may aggravate the greenhouse effect of desert areas covered with biocrusts.