Urban ecosystem has become a critical part of ecological security and draws much attention worldwide. It is both a result of natural ecological system development, and also an inevitable outcome of human ecological system development within a certain stage, with the objective of identifying the possible improvement space for unban ecological security evaluation from complex system perspective. Based on the brittle structure model and set pair theory, this paper firstly explored the main research methods of urban ecological security theory and its characteristics, then conducted a theory of complex system brittleness to analyze the urban ecological security brittle factors, brittle primitives, and brittle structure. Furthermore, it conducted a model of urban ecological system brittleness correlation entropy together with a set pair analysis method to discuss its brittleness. And finally, an ecological safety evaluation has been presented based on the empirical case in Chengdu City of China. The theoretical and empirical analysis shows that the brittle correlation entropy of natural subsystem in urban ecological security is the biggest one. The risks from natural subsystem collapse can easily trigger the brittleness of the entire urban system. The corresponding maximum brittle fluctuation entropy is from economic subsystem; it has a largest impact on the entropy change of urban ecosystem. The way of reducing the uncertainty of urban ecological risks is to lower difference degree coefficient in the system. Relevant decision makers should consider to reduce the increasing degree of entropy and eliminate the fluctuation of the brittle factors. Thus, the threats or risks of urban ecological system can be within the acceptable range and under control. An integrated system management combing with brittleness characters of natural, economics, and social subsystem is necessary. It is helpful for the ecological security construction.