We examined bulk soil properties and molecular biomarker distributions in surface soils from Inner Mongolian grasslands in order to understand the responses of soil organic matter to different land use. A total of 16 soils were collected from severely degraded grassland by overgrazing (DG), native grassland without apparent anthropogenic disturbance (NG), groundwater-sustaining grassland (GG) and restored grassland from previous potato cropland (RG). Compared to NG, soil organic carbon content was lower by 50% in DG, but higher by six-fold in GG and one-fold in RG. The delta C-13 values of soil organic carbon were -24.2 +/- 0.6 parts per thousand in DG, -24.9 +/- 0.6 parts per thousand in NG, -25.1 +/- 0.1 parts per thousand in RG and -26.2 +/- 0.6 parts per thousand in GG, reflecting different degradation degrees of soil organic matter or different water use efficiencies. The soils in DG contained the lowest abundance of aliphatic lipids (n-alkanes, n-alkanols, n-alkanoic acids, omega-hydroxylalkanoic acids and alpha-hydroxyalkanoic acids) and lignin-phenols, suggesting selective removal of these biochemically recalcitrant biomarkers with grassland degradation by microbial respiration or wind erosion. Compared to NG, the soils in GG and RG increased omega-hydroxylalkanoic acids by 60-70%, a biomarker for suberin from roots, and increased alpha-hydroxylalkanoic acids by 10-20%, a biomarker for both cutin and suberin. Our results demonstrate that the groundwater supply and cultivation-restoration practices in Inner Mongolian grasslands not only enhance soil organic carbon sequestration, but also change the proportions of shoot-versus root-derived carbon in soils. This finding has important implications for the global carbon cycle since root-derived aliphatic carbon has a longer residence time than the aboveground tissue-derived carbon in soils.