In the hinterland of deserts, it is difficult to reconstruct paleovegetation using fossil pollen because of the low pollen concentration. Therefore, an efficient method is needed to reconstruct the paleovegetation of desert regions. In this study, 34 Holocene calcareous root tube (CRT) samples were collected from the Alashan Desert in northwest China, and lipid molecular proxies from CRTs were selected to address this deficiency. The results show that n-alkanes mainly maximized at C27, C29, and C16, and that the carbon preference index is close to 1. Thus, the sources of n-alkanes from CRTs were the roots of higher plants and microorganisms, and thus changes in n-alkanes from CRTs could reveal variations in vegetation cover. The n-alkane Cmax of long-chain n-alkanes (C>25) in CRTs, maximizing at C27, indicated that vegetation in the Alashan Desert was characterized by shrub vegetation during the Holocene. Changes in the ratio of (C27+C29)/(C31+C33) indicated that the biomass of shrub vegetation increased during the period 7–2 cal ka BP. Moreover, the relative concentration of short-chain to long-chain n-alkanes decreased from 7 to 2 cal ka BP, suggesting that the effective moisture decreased during that period.