Due to their long-term dual structures and rapid urbanization, cities and villages in developing countries are undergoing the challenges of urban-rural integration and ecological security. This study aims to determine the pattern of urban-rural spatial structures under the circumstances of ecological security in the future to promote the integrated, coordinated, green, and sustainable development of urban-rural spaces. Using a quantitative evaluation method, the logistic-CA model, the LCP (least cost path) model, and a classification of ecological importance, this study constructed an integrated simulation model based on a green infrastructure assessment and applied the model to simulate and predict the urban-rural spatial structure of the Harbin city territory (Harbin) in 2035. The results indicate that the urban-rural hierarchical scale structure of Harbin comprises a central city, sub-central city, central town, major town, common town, central village, and general village. The urban-rural traffic network structure forms a pattern of “radiation + grid”, with Harbin city at the center of the structure. The urban-rural land use zoning structure consists of eco-spaces, agricultural spaces, and construction spaces. It can be concluded that in 2035, the urban-rural spatial structure of Harbin will show an increasing development tendency, where single-center, medium, and small cities in will Harbin develop, and traffic systems above the county level will also improve.