Along with the quick development of global industrialization and urbanism, cities have become the position of human technology progress, economic development and social civilization, which are also the focus place of environment pollutions, ecological destruction and social problems. In the recent several years, while developing countries are urbanized greatly, some problems are showed, such as populations increasing greatly, environment pollution, translation hustles, confusion of the building landscapes and lack of uniform devising development and so on, then "city becomes the most important problem among all environment problems", city sustainable development research becomes the world's concern. Therefore, there is great theory and practical valuable about how to explain and evaluate the complex system evolvement regulation of urban ecosystem and solve the main problem it facing, in the further to realize the sustainable development of urban and area social economic, which according to the urban ecology principle and the application of system scientific methods.The problem about the monitor and early-warning of urban ecosystem sustainable development is studied in this paper, which is based on the application of the views and thinking of system science and system project. The main contents include:Firstly, According to the summarization of former related researches, the theories foundation about urban ecosystem research is studied and the history evolution progress of urban ecological thinking is summarized. The contents about urban ecosystem's meanings, character, elements, construction and function are discussed. According to the modern system science theory, the circulation mechanism of urban ecosystem is discussed. The circulation track and evolution model of urban ecosystem are bring forward in the view of entropy theory and control theory.Secondly, the concept and content of urban ecosystem monitor and early-warning are set forth. The indexes system of urban ecosystem monitor and early-warning are designed. The idea of urban ecosystem early-warning is put forward and the structure of urban ecosystem monitor and early-warning system is built.Thirdly, the BP neural network model for forecasting is built based on artificial immune optimization. A urban ecosystem monitor and early-warning model is brought forward based on the grey related analysis which is improved on.At last, the urban ecosystem monitor and early-warning model is used for Nanjing urban's monitor and early-warning research on the base of analyzing the current state of Nanjing ecosystem, and the results are analyzed.