Ecoregion and its classification systems are increasingly used for enactment of environmental protection policies and management decision, particularly in management, conservation and assessment of natural resources. A number of ecoregion and its classification systems are currently available in the world, with each system defining ecoregions using different classification methods and different types of indices. How to accurately appraise and choose these systems for managing natural resources and environmental decision puzzles the managers and researchers. In this work, the current situation and international advancements of research on ecoregion classifications in the past two decades were summarized, and the differences between main ecoregion and its classification systems in USA and eco-functional regionalization in China were emphatically compared and analyzed. The results indicated that there were remarkable differences in subarea unit connotation, emphases and subarea angles of ecoregions between China and USA. In USA′s ecoregion and its classification systems, more attention has paid to natural ecosystems. Particularly in the assessment indexes, human beings are regarded to be on the equality with other organisms in ecosystems. On the contrary, China′s eco-functional regionalization gives prominence to the footing of human beings in ecosystems and ecological service function provided for human society by ecosystems. These systems have their merits and limitations. Thus, it will provide with references and suggestions for subsequent study on aquatic ecoregions in China and improving China′s eco-functional regionalization through comparative study on these systems.