Despite vast areas of desert soils distributed extensively in arid and semiarid regions of northern China, methane (CH₄) uptake was sparsely observed in these soils. In this study, we selected a fenced sand land of the Xilin River basin in Inner Mongolia as a case to understand in situ CH₄ uptake by desert soils. A set of measurements was made using a static chamber technique both to quantify temporal and spatial CH₄ uptake and to examine the effect of environmental factors on the uptake. The CH₄ uptake had large temporal and spatial variability during the growing seasons of both years 2009 and 2011, with a mean rate of − 48.5 μg m^{− 2} h^{− 1}. Vertical CH₄ uptake coincided with the change in CH₄ concentrations along various soil horizons, with the most active in the 5–30 cm soils. The dependence of CH₄ uptake on soil temperature and moisture was well established in these desert soils. The CH₄ uptake was temporarily enhanced over brief periods when desert soils were wetted. In order to more availably estimate in situ annual CH₄ sink in arid and semiarid regions of northern China, it is suggested that year-round measurements should be centralized on the effect of soil temperature and moisture on the CH₄ uptake.