In terms of the county area, widening the concept application of main functional areas and exploring the spatial allocation efficiency of land resources and its control strategies are of great significance to deepening China's territorial space governance system. This paper combs the theoretical relationship between main functional areas and land resources spatial allocation, the spatial allocation efficiency of land resources in main functional areas of Ganyu district, a typical county-level unit in Jiangsu province, was investigated with the C-D production function, and the differentiated control strategy was put forward. The result shows that the essence of main functional areas construction is "based on land", and land resources spatial allocation should follow the transformation degree of equal marginal net income based on the concept of functional zoning, which makes it possible to improve land efficiency and reduce the efficiency loss of spontaneous competitive advantage. A study of Ganyu district found that the excessive allocation of agricultural land to development land in different main functional areas has the pareto improvement space, which is rooted in the inelastic mechanism of the current land planning management to regulate the spatial land use index, resulting in the spatial mismatch in the actual landing. Therefore, the effective allocation of land resources in Ganyu should be based on the overall planning of main functions and the coordination of land space development pattern, including: optimizing development areas should renovate the spatial structure of land and transform the mode of economic and industrial development; key development areas will contribute to the industrialization of cities and towns and ensure the efficiency of land resources use in the region; restricted development areas focus on the safety of grain and economic products and innovate the management mode of agricultural production land; prohibited development areas draw the red line of ecological space in development zones and explore the layout and structure of agricultural and tourism ecological land.