With accelerating urbanization in China as well as in the world, the profound environment impact of urban land has been concerned because urban system consumes large quantities of natural resources and releases large quantities of wastes which contain pollutants. The natural resources over-exhausted and air and water pollution seriously deteriorated the urban and suburban environments humans reside in. The degradation in urban environment has attracted the interests of ecologists in the last three decades. The ecology in cities has been developed to ecology of city. The latter as a holistic study focuses on the structure, pattern, process and function of urban ecosystem. It is widely recognized that urban ecosystem is a human-dominated system with artificial infrastructure, higher density of inputs and outputs of energy and materials, artificial path and human-controlled transportation of energy and materials and high efficient of social and economic production. In 1997, two long-term ecological studies programs initiated in Baltimore and Phoenix supported by National Sciences Foundation USA. In 2001, Beijing Urban Ecosystem Research Station was initiated to monitor and investigate environmental changes in Beijing. In this paper, we reviewed the research framework of urban ecosystem developed in recent years, and compared the Phoenix, Baltimore and Beijing long-term urban ecosystems studies in terms of goal, basic scientific principles, themes and methodology. The investigation of urban ecosystems should combine social-economic and natural physical templates, study the changes in structure and function of urban ecosystem under short-term pulses and long-term stresses, assess these changes effects on ecosystem services, and formulate policy to manage and regulate urban systems. Beijing Urban Ecosystem Station would aim to understand the evolution of structure-pattern-process-function and to provide scientific basis for preventing water shortage and environmental pollution, raising living quality, and improving social and economic development, by deploying remote sensing technology, long-term plots survey, long-term stationary and mobile monitoring and social survey, monitoring the structural and functional indicators of urban ecosystem, investigating long-term evolution of urban ecosystem, energy and materials flows of urban ecosystem, water resource and utilization, and environmental response of urban organism, and building eco-planning, eco-management and eco-engineering demonstrations for urban sustainable development. Innovations of theory and methodology in urban ecology and coupling physical and human processes in urban ecosystem are important issues for long-term studies in the future.