Urban agglomeration ecological conservation and regional ecological security depend on the identification of ecological conservation priority areas. The identification of ecological conservation priority areas in urban agglomerations based on ecological conservation importance evaluation aids in ensuring the supply level of ecosystem services as well as maintaining the stability of ecosystems from the external functional dimension and internal stability dimension of ecosystems, thereby upholding regional ecological security and preserving human welfare. On the basis of the evaluation of ecological conservation importance, there are currently no techniques to identify ecological conservation priority areas in urban agglomerations by merging ecosystem service indicators and ecological vulnerability indicators, as well as the use of an ordered weighted averaging (OWA) operator combined with an objective weighting method. In the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), a new indicator system for evaluating the ecological conservation relevance was established by incorporating ecosystem service indicators, such as food production and carbon storage, and ecological vulnerability indicators, such as land use intensity, heavy rainfall days, and acid rain sensitivity, in order to balance out one-sided evaluation findings brought on by the removal of some ecosystem service values or critical ecosystem services. Then, using a combined subject-objective assignment method that blended spatial principal component analysis (SPCA) and OWA, the ideal scenario was selected based on conservation efficiency and tradeoff. With a trade-off degree of 0.6837 and a conservation efficiency of 1.0553, scenario 4 was determined to be the best option. In this case, the ecological conservation priority area's overall ecological conservation value is comparatively the highest, and the potential evaluation inaccuracy brought on by the issue of indicator trade-offs is somewhat mitigated. The priority ecological conservation areas of the GBA covered a total area of 26,406.04 km², or 47.69% of the GBA's total land area. The majority of them were situated in areas outside the GBA's central region, including Zhaoqing, Huizhou, Hong Kong, the northern part of Guangzhou, the outer ring of Jiangmen, and the eastern coast of Shenzhen, among others. The red ecological protection line and the bulk of the surrounding general ecological space were effectively covered by the ecological conservation priority areas. This paper proposed a new technique for selecting ecological conservation priority areas in urban agglomerations, which can provide a theoretical framework and technological support for towns and urban agglomerations sustainable ecological development and regional ecosystem management, so as to successfully maintain the regional ecological security of urban agglomerations while better protecting and promoting human welfare.