This study investigated the enrichment and fractionation of rare earth elements (REE) in soils with different soil organic carbon (SOC) concentrations under diverse land uses. The results indicated that there were significant and important differences in soil REE behavior. Their fractionation was strongly and negatively correlated to the middle REE (MREE) and SOC implying that soil organic matter (SOM) acts as the host phase for the REE. Higher total REE concentrations in sites dominated by C4 plants than those dominated by C3 plants, and the significant negative correlation between d13C and MREE indicated that the organic functional groups that adsorb REE change with the stable isotope composition of SOC. This observation demonstrates the potential use of REE for tracing natural influences on behavior of SOC in the profiles of SOC-rich soils.