Currently, CUES offers eight MS degree programs, including Physical Geography, Human Geography, Historical Geography, Geomorphology, Quaternary Geology, Environmental Science, Urban and Regional Planning, and Ecology, and six Ph.D. programs, including Physical Geography, Human Geography, Historical Geography, Geomorphology, Environmental Geography, and Quaternary Geology.
The main focus of the Physical Geography program is to study the interaction between human beings and nature, thus providing students with the tools needed to understand how this interaction modifies the environment at both the local and global levels. The program covers a broad spectrum of topics, including land science, global environmental change and terrestrial ecosystems, natural resource management and regional development, regional ecological security and risk, land use and landscape ecology, and integrated watershed management, all of which are aimed at providing a better understanding of the physic-geographical system and improved management of human interaction with the natural system. Research activities focus on integrated research on global environmental change and its regional responses. Technical skills in geographical methods, such as remote sensing, GIS, spatial analysis and modeling, and data visualization, are integrated with substantive training for studies framed within physical factors and/or human-environment interactions. Physical geography is a field-oriented discipline, thus field survey and sampling training are particularly emphasized in the program.

The Human Geography program studies the geographical patterns of human activities in contemporary China, with a special focus on economic geography and urban geography. The program employs both quantitative and qualitative methods to explore the interactions between humans and space. Within this program, urban geography focuses on urbanization/suburbanization, urban hierarchy, urban land use, spatial structure and social geography in cities, providing theoretical and technical supports for urban and regional planning, land use planning, and strategic planning. Economic geography studies industrial location theory, regional development theory, regional innovation system, land development, industrial clusters/agglomeration, globalization /localization, multinational corporations, and industrial ecology. It also provides strong  scientific support for regional and local development policies in China.

The focus of the Environmental Geography program is the study of regional fate and effects of various pollutants for addressing strong public and administrative concerns on the deterioration of environmental quality during the rapid economic development. The program relies on both modern analytical instrumentation for analyzing low concentration toxic pollutants in various environmental media and on the  modeling technique for quantifying the fate of pollutants at regional and global scales. Within this program, environmental toxicology  encompasses bioavailability and ecological risk assessment on persistent organic pollutants and endocrine disruptors in the environment, as well as human exposure to these pollutants. Regional environment focuses on the spatial patterns of emission, transport and distribution of various pollutants, and the policy dimension of environmental issues.

The Ecology program focuses on regional and global vegetation and their relation to global climate change, carbon and water cycle, biodiversity, and ecosystem functions. The program relies on long-term observation and controlled experiment, large-scale vegetation survey, remote-sensing observation for analyzing carbon and nitrogen cycle in different terrestrial ecosystems, as well as modeling technology for predicting future dynamics of vegetation and ecosystem services under changing climates. Within this program, global changing ecology theme focuses on global and regional carbon cycles; Vegetation ecology theme focuses on plant community theories and vegetation dynamics at different time-scales during the Holocene; Biodiversity theme aims at detecting patterns and drivers of plant biodiversity at country, continental, and global scales; Landscape ecology theme devotes to urban and regional development in China by applying ecological principles and methods.

Research in the Quaternary program is directed at advancing our understanding of Earth`s environmental changes during the past 2.5 million years. Terrestrial and marine sediments from different regions are collected and investigated using physical, chemical, and biological methods for quantitative reconstruction of the past environments at different timescales. Most of the scientific works focused on two areas of improvement of dating methodologies for past global change research, and development of proxies for paleoenvironmental study.

Traditionally, research in Historical Geography looks into geographical changes through time in order to reconstruct past phenomena and processes through researching information from ancient Chinese literature. For this, sound training in classical Chinese literature is critical. The main topics interested include historical changes in the utilization of human and natural resources, the form and functions of human settlements and built environments, evolution of geographical patterns of physical environments and human activities. Recently, the introduction of model analytical techniques and a combination of information from Chinese literature and results of modern instrumental analysis have provided an exciting new approach in this area.

In addition, CUES offers a three-year, full-time professional M.S. degree program in Urban and Regional Planning. The program aims to educate planners with a broad range of skills in urban and regional planning and balance human well-being, environmental protection, social justice and urban and regional sustainability in policy-making, and research fields. Some courses in this program include urban planning, urban design, land use, housing, heritage study, tourism planning, landscape architecture, and human geography. In addition, research methods and urban planning studio experience.