The relative contribution of roots versus shoots to soil organic carbon (SOC) is a long-debated topic related to soil carbon formation and dynamics. However, the variation of root-and shoot-derived carbon in natural soils remains poorly constrained due to limited tools to separate them. Here we overcome the difficulty by analyzing biomarkers for root (suberin) and shoot (cutin) in grassland soils spanning >7,000 km on the Qinghai-Tibetan and Mongolian Plateaus. Coupled with a comprehensive list of climatic, edaphic, and vegetation variables, we assess their inputs, distribution, and preservation patterns. We find that while suberin was a root-specific tracer, cutin biomarkers that occurred only in trace amount in roots also had a minor but nonnegligible contribution from belowground sources due to the massive root mass in the alpine grasslands. Both components had higher SOC-normalized concentrations in the alpine than temperate grasslands, along with a higher preservation percentage against net primary productivity and a lower degradation parameter, suggesting a better preservation of these plant-derived lipid components in the alpine region. Moreover, while cutin and suberin abundances were affected by plant inputs and other SOC constituents, the root mass normalized incorporation efficiency of suberin was only positively correlated to SOC in both regions with a steeper slope in the alpine grasslands and also negatively correlated to root mass in the alpine soils. These results imply that root carbon incorporation is sensitive to environmental variations in the cold region, suggesting potentially more dynamic alterations to root carbon sequestration with environmental changes.