Forest ecosystem plays an important role in regulating global carbon cycle and climate change, to estimate its carbon storage, this study selected five major forest types in Northeast and investigated its tree, understory vegetation, forest floor and soil carbon density based on field measurement. Subsequently, we combined with the 7th Forest Resources Statistics of China to calculate forest carbon storage under the natural forest protection program in Northeast on regional scale. Results showed that forest ecosystem carbon storage under the natural forest protection program in Northeast was 4603.8 TgC, in which tree, understory, forest floor and soil carbon storages account for 22.7%, 0.9%, 6.5% and 69.9% respectively. Forest ecosystem carbon density was 180.6 Mg/ha, and tree, understory, and forest floor carbon density all increased with age class, which imply the great forest carbon sequestration potential under the natural forest protection program in Northeast.