With natural space shrinking and the ecological environment deteriorating, the conflict between economic development and environmental protection is increasingly intensified. As urban areas expand, land for construction (treated as a special resource) consumes natural areas, resulting in negative impacts on the environment, while having a positive effect on economic development. The challenge in the allocation of construction land resources is that it must consider both environmental protection and economic development. The traditional strategy of resource allocation based solely on efficiency only satisfies the objectives of economic development, and ignores the significant ecological constraints on socio-economic development, leading ultimately to an unsustainable development of society and the economy. Therefore, in planning for construction-land allocation, environmental protection and economic efficiency must be balanced. To mediate the conflict between economic development space and ecological protection space-achieving sustainable economic development and environmental protection-this paper examines the optimum spatial allocation of construction land using the landscape ecology methodology and economic principles, from an eco-economic comparative advantage perspective. First, a comprehensive regional ecological security pattern was developed using the landscape security pattern method, allowing us to calculate the ecological importance indexes of space units according to the security pattern. Using the minimum cumulative resistance model, the economic suitability index of regional construction land development was evaluated. This was the basis for economic suitability indexes of construction land development for the spatial units. Second, we calculated the comparative advantage index of construction land development based on the ecological importance index and the economic suitability index. We then built a construction land allocation model (solved by the Monte Carlo Method), the objective function of which is to optimize the space constraints of comparative advantage satisfaction. Finally, we applied our empirical research, using Yangzhou City of Jiangsu Province as an example. Research results indicate that in the future the construction land of Yangzhou would concentrate on the developed southern area of the city, while the northern part of the city primarily plays a role in environmental protection. The allocation of construction land reflects the dislocation pattern of economic development and ecological protection, which could benefit both economic development and environmental protection in Yangzhou City. Meanwhile, using the grid as the smallest unit to evaluate both the ecological importance and the economic suitability of construction land, the planners and decision makers can better understand the spatial continuity and the non-equilibrium of natural and economic elements. This understanding will play a strong guiding role on the spatial layout of construction land. Additionally, to estimate land development intensity for each administrative unit, the proposed resource allocation model combines numerous factors of basic farmland protection and land resource endowments. This provides a scientific method and theoretical basis for the determination of land development intensity. This research proposes a method of optimum spatial allocation of construction land from an eco-economic comparative advantage perspective, and provides a scientific basis for both land-use and environmental protection planning.