Soil salinization is common phenomenon in Songnen Plain of northeast China, which seriously restricts the development of agriculture. Long-term manure application can significantly increase the content of soil organic carbon, which is the major method for saline-sodic soils amelioration. According to the cattle manure application history, manure applied to saline-sodic soils for 5, 9 and 16 years were used as the experimental treatments, and soil without manure application was used as a control. Based on long-term experimentation, soil δ13CSOC value, soil organic carbon fraction, corn yield, soil pH and soil EC were determined. The relative contribution of plant residue and organic manure to soil carbon sequestration was quantified. Furthermore, the distribution ratio of soil organic carbon fraction was explicit. Simultaneously, the characteristic of soil organic carbon fraction distribution were discussed in saline-sodic soils. Our results indicated that corn (Zea mays L.) with long-term manure application significantly (P<0.05) increased the δ13CSOC value in saline-sodic soils (P<0.05), and δ13CSOC was increased with the duration of manure application. On the other hand, the contribution of corn-derived carbon (below-ground roots and residues) and the manure-derived carbon to soil organic carbon can be calculated from δ13CSOC value of plant and soil by using a two-end member mixed model. Our results showed that after nine years manure application, corn-derived soil organic carbon comprised about 14.36% of total soil organic carbon and manure-derived soil organic carbon accounted for 25.92%, and the other part was from original soil organic carbon of saline-sodic soils. Long term manure application significantly resulted in an increase in corn yield and decreases in soil pH and EC, and corn yield increased with the number of year of manure application. Conversely, soil pH and EC decreased with the number of year of manure application. Generally, soil organic carbon can be chemically divided into labile I, labile II and recalcitrant carbon that have different sensitivities to changes of environmental conditions. Changes in SOC fractions may provide an early indicator of changes in total SOC. Long-term manure application also significantly increased the density of each soil organic carbon fraction, and the density of soil organic carbon fractions, such as labile I carbon, labile II carbon and recalcitrant carbon, was increased with the number of year of manure application at the 0-20 and 20-40 cm, respectively. The density of soil organic carbon fractions was the highest in the treatment with manure application for 16 years. Increased contents of soil organic carbon was most contributed by soil recalcitrant carbon and soil labile II carbon, followed by soil labile I carbon at the 0-20cm and 20-40cm, respectively. Summarily, long-term manure application can directly enrich the carbon source of plant, promote the long-term sequestration of soil carbon, and enhance the carbon sink function of saline-sodic soils. Long term manure application was necessary to a win-win strategy for both SOC sequestration and corn production. The contribution of manure derived carbon to SOC increase was larger than corn derived carbon.