Urban agglomerations, as emerging competitive geographical units in the era of globalization, grapple with the challenge of reconciling rapid urbanization and ecological dynamics, thereby influencing regional sustainability. This predicament is particularly pronounced in dual-core urban agglomerations like Chengdu-Chongqing, necessitating a delicate balance in their interplay. Our study establishes an assessment framework for the synergistic development of ecological environments and urbanization in dual-core urban agglomerations. Leveraging Remote Sensing and Geographic Information System (GIS) techniques, we conduct a multiscale analysis of urbanization and ecological environment synergies. Our findings reveal that: 1) Over the past two decades, the ecological quality of Chengdu-Chongqing urban agglomeration has exhibited a fluctuating yet ascending trend, with nighttime light data indicating continuous and rapid urbanization. 2) The synergistic development of the dual-core urban agglomeration unfolds in distinct stages, influenced by cyclical national policies and unforeseen natural disasters during 2005–2015. Scale differences in the degree of coordinated development within urban agglomeration necessitate strategic differentiation. 3) The trajectory of dual-core urban agglomeration development persists, revealing conspicuous intraregional gaps that, if excessively disparate, could compromise sustainable regional development. This study not only offers scientific decision support for the dual-core urban agglomeration’s development but also advances regional ecological civilization, providing developmental insights for analogous urban agglomerations worldwide.