In geographic research, regionalization is an effective measure to understand the regional differentiation of geographical environment and optimize the structure and function of regional man-land system. Based on the existing research, we firstly define the concepts of regional ecological economics, which is a new interdisciplinary subject, as well as the concepts of eco-economic regionalization, and put forward five principles of eco-economic regionalization. Then, it is the first time for us to establish a two-level program to explore the eco-economic regionalization of the China-Mongolia-Russia economic corridor, one of the most important economic growth corridors in China, Mongolia, and Russia. We use systematic cluster analysis to reveal the spatial distribution pattern of physical geographical factors such as landforms, precipitation, temperature, and human economic factor such as the intensity of human activities, and firstly divide the 48 regions of the China-Mongolia-Russia economic corridor into six types of eco-economic zones, namely, I. Eastern European Plain eco-economic zone, II. West Siberia Plain eco-economic zone, III. Central Siberia Plateau eco-economic zone, IV. Russian Far East Mountain eco-economic zone, V. Northeast China Plain eco-economic zone, and VI. Mongolian Plateau eco-economic zone. Then, we introduce specific eco-environment factors such as land use type, environmental pollutant emissions, and socio-economic factors such as industrial structure, urbanization rate, GDP per capita, GDP growth rate, and fixed capital investment per capita. We apply entropy to evaluate the eco-environment and socio-economic development of the 48 regions of the China-Mongolia-Russia economic corridor, and further divide the six eco-economic zones into 19 eco-economic sub-zones according to the spatial distribution of eco-environment and socio-economic development of the 48 regions. We comparatively analyze the characteristics and the regional differentiation of the eco-environment and socio-economic development of these 19 eco-economic sub-zones, and classify them into three development categories, namely, optimized development zone, key development zone, and conservative development zone. Finally, we put forward targeted suggestions for the green development of each category. This study will provide scientific support for the green and high-quality development of the China-Mongolia-Russia economic corridor.