Eco-city and green building are the global development strategies today. In order to improve the management level of green buildings in the urbanization process, a reciprocal symbiosis evaluation index model is proposed based on the theory of urban ecology. On this basis, the collaborative relationship model between Eco-city and green building is established, and the green building management framework based on the collaborative theory is constructed. The expert survey method was used to determine the evaluation indicators and analyze the relationship between various city subsystems. Then, the analytic hierarchy process is used to build a three-level evaluation index system, including the target layer, the criterion layer, and the index layer. The weight of the evaluation index system is calculated by combining of the chromatography method and the entropy weight method, and a scientific evaluation index system is established. The gray comprehensive evaluation method is used to evaluate the construction of the green building management system. Based on the index system, the analytic hierarchy process is used to calculate different weight coefficients, which makes the evaluation model easy to use and lays a foundation for subsequent research.