Abstract: Long-term fertilization experiments were carried out to study variations of organic carbon contents and carbon storage in the profiles (0-100 cm) of black soil and grey desert soil. The results show that compared to the initial values of carbon contents, the contents of organic carbon in soil depths of 020 cm and 2040 cm can be improved obviously by applying chemical fertilizers combined with manure (NPKM2), and increased continuously with the fertilization year by year. After 20-years application of NPKM2, the contents of organic carbon in soil depths of 020 cm and 2040 cm are increased by 56.6% and 49.6% in black soil, and 143.1% and 46.9% in grey desert soil, respectively. The carbon contents in soil depths of 020 cm and 2040 cm by applying NPKM increased are less than those of applying NPKM2, which are increased by 35.1% and 35.3% in black soil, and 143.1% and 46.9% in grey desert soil, respectively. The organic carbon contents in soil depth of 40100 cm arent changed obviously under various fertilization conditions. The applications of chemical fertilizers and CK could keep the organic carbon contents in soil depth of 0100cm in black soil, while the organic carbon contents are slightly reduced in grey desert soil. Both applications of NPKM and NPKM2 can increase the organic carbon storages in soil depth of 0100 cm obviously in black soil and grey desert soil, which are increased by C 30.7t/ha and C 40.6 t/ha respectively, and the application of NPKM2 can improve the organic carbon storage more obviously. In conclusion, the applications of NPKM or NPKM2 can improve the contents of organic carbon in soil depth of 040 cm, and can also increase organic carbon storages in soil depth of 0100 cm.