Abstract: β diversity is an important index characterizing composition variation of vegetation community. The southern part of Gurbantunggut Desert is taken as the study area in this paper, on the basis of vegetation survey in 67 plots, β diversity variation of vegetation community in the study area is analyzed first in longitudinal and latitudinal directions, and then the method of variance partitioning is used for analyzing contribution ratio of environment variable, soil seed bank variable and spatial variable to β diversity differentiation, discussing the mechanism of β diversity differentiation of desert vegetation. It is shown with the results that β diversity is an increase of species similarity from west to east in longitudinal direction, and the species succession rate declines; a decrease of species similarity from north to south in latitudinal direction, and the species succession rate increases slightly. Regarding interpretation of β diversity differentiation, the environment variables such as 30-year’s average monthly precipitation play a decisive role in distribution of desert vegetation community, while the interpretation ratio of soil variable and spatial variable are relative low. Comparing with soil heterogeneity, the variation of soil seed bank has a bigger impact on β diversity differentiation. The main environmental variables, soil variables effect were scale dependent. Neutral process determined by the spatial structure also plays a role. It is found out that although environment variables (including soil variable), soil seed bank variable and spatial variable are taken into consideration, nearly 50% of β diversity differentiation cannot be interpreted, which indicates that some other environment variables and random process have impact on the variation of vegetation community.