Ecotones exhibited edge effects and were characterized by abundant endemic species, a high number of alien species, and frequent material flows, playing a crucial role in maintaining regional biodiversity. However, intensified human activities increased habitat fragmentation in these areas, impeding species migration and dispersal, and had a negative impact on biodiversity conservation. Constructing ecological networks could connect isolated habitat patches, mitigate habitat fragmentation, and enhance species dispersal capacity. Existing studies on ecological network construction in ecotones often relied on administrative boundaries as the research extent, which negatively affected the accurate identification of species' migration patterns across source areas. This study took Datong City, a typical ecotone region, as a case study to construct three spatial scenarios: administrative zone, buffer zone, and ecotone zone. Methods such as Conefor 2.6, MSPA, and Linkage Mapper were employed to extend the methodology of scale-nested ecological network systems. By incorporating corridors, sources, and nodes that intersected with administrative boundaries, a multi-scale nested ecological network system for the ecotone was developed. The results showed that: (1) Under various buffer scenarios, the core area remains relatively stable when the expansion distance is within 40 km, followed by a significant upward trend thereafter; (2) Under the 50 km buffer zone scenario, the connectivity characteristics of source landscapes, network structural features, and centrality of source-corridors remained relatively stable, making it a representative buffer zone scenario; (3) In both the representative buffer and ecotone scenarios, the centrality of sources and corridors intersecting administrative boundaries was comparable to or higher than that of all sources and corridors, indicating a high level of contribution to the ecological network; (4) In the constructed ecological network system, the administrative zone scenario included 53 core source patches and 46 additional sources, 221 basic corridors and 46 intersecting corridors, with a total of 82 intersecting nodes. This highlighted clear differences between the scale-nested ecological network system and traditional perspectives. This study extends the framework of scale-nested ecological network construction, emphasizing the critical role of intersecting elements, and provides a methodological approach for constructing ecological network systems that accurately reflect species' actual migration patterns in ecotone regions. The findings contributed to biodiversity enhancement and provided decision-making support for constructing nested ecological network systems at the regional scale in ecotones. Specifically, the classification and hierarchical management of various ecological elements, along with the delineation of management scopes for intersecting nodes, can provide a scientific basis for targeted and effective ecological planning.