To understand the biogeochemical processes associated with soil organic matter (SOM) decomposition, we analyzed the SOM contents, the δ13C and δ15N values of the dominant species foliage, litter and SOM from soil samples for five soil profiles with different vegetation conditions in the Loess Plateau, Northwestern China. Results showed that the amounts of soil organic carbon (SOC) and total nitrogen (TN) mainly concentrated on the surface soil and differentiated according to the vegetation conditions in the following order: broad-leaved forest > coniferous woodland > shrub forest > grassland > wasteland. SOC and TN contents decreased with depth and varied in the ranges of 1.1–31.2 g/kg and 0.3–3.7 g/kg, respectively. Compared with the other regions, the 13C and 15N were enriched and the δ13C and δ15N values of topsoil SOM respectively increased in the ranges of 0.5%o–3.2%o and 0.7%o–4.6%o during litter degradation to SOM on the surface soil, which was controlled by SOM turnover rates. This result indicates that the effect of isotopic fractionation was obvious during the transformation of SOM from plant debris to SOM in topsoil, which resulted in great increments of SOM δ13C and δ15N. Litter inputs lowered the surface soil δ13C and δ15N values while decomposition increased δ13C and δ15N values in deeper soil. Foliage and litter inputs averaged 1.0% and 1.3% δ15N and -28.3% and -27.0% δ13C, respectively. The five soil profiles with different vegetation conditions had similar characteristics in variations of SOM δ13C and δ15N and increased with depth, respectively. However, the patterns of δ13C in our sites were less pronounced than the patterns of δ15N primarily because the discrimination against 13C during organic matter decomposition is weaker than the discrimination against 15N. Except for the shrub profiles, significant correlations were found between the two stable isotopes, 15N and 13C. Combined with information on SOM contents, the variations of the isotopic values of SOM showed a mixing process of litter inputs between different soil profiles. Two controls of soil isotopic compositions were established: new litter inputs and overall isotopic fractionation during decomposition. In conclusion, the overall isotopic fractionation during decomposition left residual soil N and C enriched in 15N and 13C, explaining the high δ15N and δ13C values observed in deeper soil.