The carbon cycle greatly influences global change, and the land cover changes contribute to the status and rate of the carbon budget in ecosystems. This paper proposes a land cover classification system for land cover mapping for the estimation of carbon storage in ecosystems and the national environmental assessments. The classification system consists of basic land cover classes at level Ⅰ and Ⅱ, and auxiliary features at level Ⅲ. The basic 38 classes at level Ⅱ characterizing land cover features are derived from 19 criteria referring to aspects of composition, structure, pattern, phenology, etc. The basic classes reflect the status of carbon storage in ecosystems. The system defines more detail in vegetation, the criteria includes life form, vegetation height, leaf type, vegetation phenology, vegetation cover, soil disturbance under vegetation, harvest disturbance, spatial relationships between vegetation and artificial surfaces. Meanwhile, non-vegetation criteria is considered in non-vegetation types definition for large scale ecological monitoring and assessment, such as the water conditions, the artificial surface features, soil structure, land granular, soil salinity, soil moisture, surface state, the water flowing. The auxiliary classes at level Ⅲ complement the attributes of level Ⅰ and Ⅱ by 9 criteria. The 5 environmental criteria of temperature, moisture, landform, aspect and slope mainly reflect the potential and intensity of carbon storage in ecosystems. The disturbance of vegetation succession caused by land use type influences the vegetation carbon budget. The other 4 criteria of vegetation cover, vegetation growing period, land use and species characteristics further refine the vegetation types, and land use typically impact the carbon storage. The structure of the land cover map of the classes of levels Ⅰ and Ⅱ is independent of the products of level Ⅲ, which is helpful for land cover product management and applications. The classification system has been adopted in the Chinese national land cover database (ChinaCover2010) for the carbon budget in ecosystems at a 30 m scale. The classification system is characterized by the factors of intrinsic attributes and extrinsic property of land cover. It is able to effectively reflect the status of ecosystem carbon stocks, rate of change, the potential and mechanism. Classification system uses a flexible definition of vegetation cover, and it is able to re-organize vegetation classes by different vegetation coverage, this approach allows analysis and comparison on different classification system among countries or organizations. Class definition is performed by using FAO LCCS tools through dichotomy which is defined in quantified approach of land cover. LCCS method provides relatively accurate and comprehensive type definition, a priori design to make it much fair, balanced, but also makes the system extensive application. With the increasing attention to global environmental issues, land cover data used in the international exchange and comparison become more frequent, standardized LCCS will be the future application trends.