Sustainable management of multifunctional landscapes requires a clear understanding of how ecosystem services (ESs) are spatially organized and jointly distributed across heterogeneous landscape contexts. However, the structural organization and co-occurrence patterns among multiple ESs remain insufficiently explored at landscape scales. To address this gap, this study develops a network-based analytical framework by integrating spatial simulations of four key ESs-water yield, food supply, carbon sequestration, and soil conservation-with network topology metrics to characterize multi-ES linkage structures. ES linkage networks were constructed for the Loess Plateau in 2000, 2010 and 2020 to identify multifunctional linkage zones and analyze their spatial organization and landscape contexts. The results show that: (1) The ES network exhibits a consistently distinct and stable core-periphery structure, with water yield and carbon sequestration persistently occupying central positions within the linkage network. (2) The extent and configuration of multifunctional linkage zones changed markedly over time, reaching their lowest level in 2010 and recovering by 2020. From 2000 to 2020, these zones shifted from cropland-dominated to natural-vegetation-dominated patterns, reflecting the influence of large-scale ecological restoration. (3) Although the proportion of cropland within linkage zones declined, cropland remained an important structural matrix supporting inter-ES linkages, whereas forests, shrubs, and grasslands increasingly underpinned the spatial continuity for multifunctional synergies. This study highlights the value of a structural linkage perspective for revealing the spatial organization of ES interactions and identifying critical multifunctional landscapes. The findings offer spatially explicit evidence to support land-use optimization and ecological compensation strategies in ecologically fragile regions.