Forest ecosystem is a vital component of terrestrial ecosystems and plays an important role in mitigating the global climate change. Using GIS technology, we evaluated data collected in 104 plots and the forestry inventory data, to estimate the organic carbon storage in forest ecosystems in the Three Gorges Reservoir region, The tissues carbon content of dominant species varied between 44.59% and 54.45%, and the carbon content of forest litter ranged from 30.61% to 42.73% with an average of 36.38％. The mean organic carbon density of forest ecosystems was 117.68t?hm-2 that is lower than the average value for whole China. The average organic carbon density in vegetation layer was 24.15 t?hm-2 with the greatest density of 42.80 t?hm-2 in the evergreen broad-leaved forest. The mean organic carbon density of litter and soil was 2.74 t?hm-2 and 9.09 kg?m-2 , separately. The total organic carbon storage of forest ecosystems was about 286.14×106t, consisted of the vegetation layer (58.72×106t), litter (6.67×106t) and soil (220.74×106t). Pinus massoniana forests with the largest distribution area had the largest carbon storage of 77.24×106t, accounted for 26.99% of the total carbon storage in the region. Correspondingly, the vegetation layer, litter, and soil of Pinus massoniana forests had also the highest carbon storage of 20.70×106, 2.66×106, and 53.89×106t, compared with other forest types, respectively. The organic carbon density of forest ecosystems decreased from the southeastern area to the northwestern area. The highest density was found in Badon-Zigui,Wushan-Wuxi, Shizhi-Wulong, and southern Jiangjin. The present study revealed that both the quality and area of forest systems play an important role in determining the carbon storage. Hence, to enhance the carbon sink, it is needed to improve the forest quality and to expend the forest area.