Soil is regarded as the largest carbon pools and the key linkage in the process of the carbon cycle in terrestrial ecosystem. The global carbon balance is directly affected by the change of source or sink of soil carbon. Hence the estimation on soil organic carbon storage becomes one of the most important content in the ecological field. We found that the difference was existed among the reported results of the soil organic carbon storage from the different researchers or research scales. This difference was mainly resulted from human disturbance and the fluctuation of environmental elements (e.g. climate change) in the sampling process, in particular, the various estimating methods and background information adopted by researchers. The significance of the study on the soil organic carbon storage was raised firstly. Then the research advances and the shortcomings in the present about the uncertainties of the estimation on soil organic carbon storage were reviewed from the aspects of environmental factors (external reason) and estimating methods (internal reason). Finally, on the basis of our thorough review, the priority areas in the future about the uncertainties on the estimation of soil organic carbon storage were suggested in this paper.