Long-term monitoring is the essential method to investigate changes in ecological systems. The long-term monitoring of natural and semi-natural ecosystems has been practiced for several decades and its protocols have been accomplished. However, it is underdeveloped for the Long-Term Monitoring of Urban Ecosystem (LTMUE) that was dominated by human activities. For improving long-term monitoring of urban ecosystem, this paper will introduce the long-term monitoring practices carrying on in Baltimore and Phoenix long-term urban ecosystem studies in USA. Then, in terms of experiences of a decade monitoring practiced in Beijing Urban Ecosystem Research Station and the general characteristics of urban ecosystem, we analyzed the objectives, principles, contents and methods of LTMUE The objectives of LTMUE are to provide databases for scientists to investigate long-term changes in urban ecosystems, and study the interaction between human and nature, and for decision makers and residents to know and predict the changes that happened in urban ecosystems. In design of LTMUE, the five principles should be considered: Reasonably balancing comprehensive and key indicators monitored, focusing comprehensive and foresight indictors, infusing data government monitored, science-oriented monitoring and long-term consistence. The LTMUE includes ecological elements, pattern, processes and function monitoring. The mostly deployed methods are remote sensing, long-term plots, substation and social survey. This will be the important methodology to guide long-term urban ecosystem investigations in China.