Abstract: Territorial spatial functional zoning is a fundamental instrument for shaping sustainable development–protection patterns and improving the efficiency of land and resource use. Conventional zoning approaches, however, largely rely on identifying functional similarity or dominant land-use attributes and often lack a systematic integration of multiple management objectives, such as ecological conservation, agricultural production, and urban development. Moreover, the explicit consideration of cost–benefit trade-offs in spatial zoning decisions remains insufficient, limiting the effectiveness and operability of zoning outcomes, especially in regions facing intense land-use conflicts. Guided by the principles of systematic conservation planning, this study develops a theoretical framework for territorial spatial functional zoning based on a “goal–cost–benefit” collaborative optimization logic. The framework emphasizes the coordinated balancing of protection targets, land-use costs, and functional benefits within a unified spatial optimization process. To operationalize this framework, we integrate land-use survey data, NDVI-derived vegetation information, point-of-interest (POI) datasets, and other socio-environmental indicators. A combination of suitability assessment, landscape pattern index analysis, and a zoning optimization model (Marxan with Zones) is employed to construct a comprehensive zoning methodology. The proposed zoning system consists of both dominant functional zones—including strict ecological conservation zones, concentrated urban construction zones, and intensive agricultural production zones—and mixed-function zones, such as agroforestry mixed zones, peri-urban agricultural zones, ecological recreation zones, and multifunctional composite zones. This hierarchical and flexible structure allows for the explicit representation of both single-function priorities and multifunctional land-use demands. Jiangyin City, a highly urbanized area with pronounced conflicts among ecological protection, agricultural production, and urban expansion, is selected as the empirical case to test the applicability of the proposed framework. The results indicate that the optimized zoning scheme substantially enhances ecological representativeness and conservation effectiveness. The protection proportions of key ecosystem types, including arbor forests and shrublands, increase to above 30%, indicating a significant improvement compared to existing planning schemes. At the same time, agricultural and urban development spaces achieve moderate expansion under the prerequisite of meeting ecological protection targets. The areas of permanent prime farmland and urban development both increase relative to the current plan, while the rise in unit-area cost is controlled within 10%, demonstrating strong overall cost-effectiveness and feasibility. From a spatial structural perspective, the optimized zoning scheme exhibits higher aggregation and coordination. The aggregation index of the intensive agricultural zone increases from 71.21 to 88.5, reflecting a more compact and efficient land-use configuration. Importantly, the introduction of mixed-function zones establishes effective transition buffers between strictly protected areas and urban construction zones, which helps mitigate potential spatial-use conflicts and enhances landscape connectivity. These zones play a critical role in reconciling competing land-use demands and improving the resilience of the territorial spatial structure. Overall, this study provides a methodological contribution by extending systematic conservation planning concepts to territorial spatial functional zoning and by explicitly embedding cost–benefit considerations into zoning optimization. The proposed framework and empirical results offer practical insights for optimizing territorial spatial patterns and refining the major function-oriented zoning system, particularly in regions characterized by high development pressure and complex land-use conflicts.