Soil erosion transports light density and fine particle soil material from hills down to low-lying land areas, which can lead to carbon loss and subsequent sequestration. In the present paper, the profile distribution of soil organic carbon (SOC) and soil 13C natural abundance (δ13C) were analyzed across five geomorphic positions, distributed along a typical rolling farmland in the Black Soil region of Northeast China. The contents of particulate organic carbon (POC) and mineral-associated organic carbon (MOC) at each geomorphic position were measured with physical fraction method. The results showed that soil erosion decreased 5.3–22.4% of SOC and increased 4.0–6.1% of δ13C of surface soils at the eroding sites. At the typical depositional sites, SOC content and δ13C value in the buried surface layer were 1.5 times and 1.1 times as much as those of the current plough layer, respectively. Soil erosion did not change the POC content, but MOC content decreased by 9.3–35.2%. At the eroding sites, the coefficient of determination between soil δ13C and MOC (R2 = 0.52) was higher than that between soil δ13C and POC (R2 = 0.37). Our study indicated that soil erosion decreased SOC content and increased δ13CSOC in surface layer mainly through transferring fine sized and 13C-depleted SOC fraction. Deep burial and re-aggregation of eroded materials at depositional sites were in favor of stabilization and sequestration of SOC.