The estimation of soil organic carbon storage is very important to the research of carbon cycle. The soil organic carbon density and storage of Chongqing karst area was estimated, using the data of 1412 soil profile from the second soil survey of China and formulating fertilization for soil conditions in 2007. Integrating the soil map, land use status quo map and district map of Chongqing karst area, the index of soil organic abundance were introduced and the characteristic of soil organic distribution in different soil and landscapes were analyzed. Results showed: the storage of soil organic carbon of Chongqing karst area to the depths of 20 cm and 100 cm were 1.43×1011 kg and 3.29×1011 kg, respectively. Carbon density of 20 cm soil was 1.26-7.20 kg m-2, and carbon density of 100 cm soil was 1.43-25.72 kg m-2. The amount of soil organic carbon varied significantly at different soils and landscapes, the index of soil organic abundance of soils and landscapes at 20 cm depth ranged from 0.73-1.74 and 0.39-1.20, and that at 100 cm depth changed between 0.32-3.00 and 0.46-1.70, respectively. The soil organic carbon storage of unit area at 20 cm depth was above the average level of China, but that at 100 cm depth was below the average level of China in Chongqing karst area. In a word, the soil organic carbon storage was relatively indigent in Chongqing karst area.