In order to implement the obligation of "United Nations framework convention on climate change", all parties should develop and submit national greenhouse gas inventory. Methods of estimating the emissions and removals of Soil carbon, CH4 emissions from rice cultivation, direct and indirect N2O emissions from agricultural soil are introduced.“2006 IPCC guidelines” emphasizes that national inventories only report carbon emissions and removals from all managed land; Adoption of the six landuse categories is used，e.g. Forest Land, Cropland ,Grassland, Wetlands, Settlements and Other Land; use multilevel methods of estimation; seasonal emission factors for rice cultivation changed into daily emission factors, and cultivation period of rice is added in the method; Biological nitrogen fixation has been removed as a direct source of N2O. With the change of methods of inventories, China is facing many difficulties and challenges in developingits national greenhouse gas inventory in the future.