Ecological sources (ESOs) with high ecosystem services (ESs) supply and landscape connectivity support effective ecological conservation, which vary across conservation objectives and scales. This study divided the Yangtze River Delta Region into three scales: greater delta region, metropolitan area, and prefecture city. By integrating ESs supply, functional, and structural connectivity, we compared the spatial distribution, scale transferability, and flexibility of ESOs for two conservation objectives: integrated importance orientation and high-value areas coverage orientation. The results showed that high-value areas coverage-oriented ESOs required larger areas but exhibited greater land-use complexity than integrated importance-oriented ESOs. These differences were strongly scale- and area-dependent, being more pronounced at smaller scales and in small- to medium-sized ESOs. Large ecological spaces with high functional priority (e.g., woodland, grasslands, and water bodies) dominated the overlapping ESOs across conservation objectives and scales. This suggested that conservation strategies integrating multiple conservation objectives should prioritize large ESOs, which were more applicable at larger scales. high-value areas coverage-oriented ESOs exhibited better scale transferability. However, both ESOs achieved effective cross-scale ecological process connectivity when mediated by the metropolitan area. Flexible conservation should prioritize buffer zones, fragmented areas between ESOs, and gaps inside the ESOs. Additionally, given ESOs’ cross-administration, coordinated cross-regional conservation was required on a broader spatial scale beyond the planning area. This study compared ESOs across different conservation objectives and scales, aiming to optimize multi-scale, multi-objective, and collaborative, flexible ecological protection planning within urban agglomerations, thereby enhancing regional and urban ecological security.