The invention belongs to the field of environmental science research, in particular to a synthetic systems analysis method for evaluating an urban ecosystem. Aiming at the problems that the internal construction and the functions of the urban ecosystem can not be effectively analyzed and evaluated and subjectivity and discreteness can not be avoided by using a traditional method, the invention integrates the prior arts, such as an urban compound biological system theory, material flow accounting, biological network analysis, mathematical statistics simulation analysis, and the like into a whole. The method for simulating, estimating and analyzing the urban ecosystem comprises the following contents, such as system definition, biological network model construction, structure and function analysis, and the like. The method is suitable for analyzing the structure and the functions of the urban ecosystem, and comprehensively estimating the operation conditions of the urban ecosystem, and can be popularized in other complicated systems, such as an industry system, a consumption system and single factor systems of energy resources, water and the like.