Flat terrain and economically prosperous downstream regions face significant challenges in achieving a balance between socio-economic development and ecological preservation. The Social–Ecological System (S-ES) serves as a vital framework for quantifying the interactions between human activities and the natural environment, providing insights into the development status of regional social and ecological systems. This study utilizes the Coupling Coordination Degree (CCD) method to construct an S-ES coupling model, integrating correlation analysis, geographic detectors, and grey relational analysis to explore the driving factors influencing Social–Ecological Resilience (S-ER) coordination. The research focuses on 25 counties in Shandong Province, situated in the lower Yellow River Basin, over the period from 2000 to 2022. Key findings include (1) significant spatial clustering, with identifiable hotspots and cold spots in S-ER distribution; (2) substantial changes in S-ER CCD around 2010 and 2020; and (3) persistent mismatches between socio-economic development and ecological improvement, presenting a major challenge for enhancing coordination. These insights provide valuable guidance for sustainable development strategies in the lower Yellow River Basin.