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At present, some regions are facing the challenge of environmental degradation, especially in the Pearl River Delta urban agglomeration (PRDUA) which is the most economically-dynamic regions in China. The PRDUA has the characteristics of high comprehensive development level and regional development inequalities, further enlarging the complexities and difficulties in assessing the ecological security. Therefore, we established an ecological footprint (EF) model of urban agglomerations and an extended nonlinear STIRPAT model to explore the spatiotemporal evolution patterns and driving mechanisms of the ecological footprint in the PRDUA, subsequently predicted the impact of population changes on the ecological footprint from 2000 to 2100 using Shared Socioeconomic Pathways scenarios (SSP1-SSP5) database. The findings reveal that the ecological footprint increased significantly, but the average annual growth slowed down after 2014. Simultaneously, the ecological footprint had a phenomenon of spatial aggregation, and gradually migrated to Shenzhen. Growing population contributed most to the expansion of the ecological footprint, followed by per capita GDP and urban green area, while there was uncertainty about the impact of technology on the ecological footprint. Further, our study also demonstrated that the classical Environmental Kuznets Curve (EKC) hypothesis did not exist between economic development and ecological footprint in the PRDUA. Finally, the results of the prediction show that ecological footprint contributed by population changes in most cities of the PRDUA peak in 2040–2060, of which the largest peaks in SSP5 scenario. The findings are intended to provide references for other urban agglomeration in the world, which are with the problem of unbalanced development between economy and ecology. • EF of the PRDUA increased significantly, but the growth slowed down after 2014. • EF has a phenomenon of spatial aggregation, and gradually migrated to Shenzhen. • Growing population makes the largest contribution to EF, while there is uncertainty about the impact of technology to EF. • EF contributed by population changes in most cities of the PRDUA peak in 2040-2060. [ABSTRACT FROM AUTHOR]