The sustainable development of urban agglomerations depends on the effective coordination of water, energy, food, and ecology (WEFE) systems. However, disparities in resource endowments and socio-economic conditions create challenges for achieving a balanced WEFE system across urban regions. This study examines three urban agglomerations in China with distinct development gradients: the Pearl River Delta (PRD), the Hohhot–Baotou–Ordos–Yulin (HBOY) region, and the Central Jilin Province (CJP). A comprehensive evaluation index system is constructed to assess the coupling coordination degree (CCD) of the WEFE system from 2008 to 2022. Through the CCD model, spatiotemporal evolution trends are analyzed, while correlation analysis explores development patterns under varying gradient conditions. A back-propagation artificial neural network (BPANN) model identifies the primary driving factors influencing WEFE coordination. Key findings include the following: (1) the CCD of the PRD, HBOY, and CJP urban agglomerations has improved over time, with CCD values ranging between 0.4 and 0.6, 0.3 and 0.5, and 0.4 and 0.6, respectively. (2) The CCD exhibits a negative correlation with urbanization rates exceeding 70% and industrialization rates but shows a positive correlation with per capita GDP. (3) The dominant contributing subsystems vary; ecology in the PRD (28.76%), food in HBOY (28.83%), and food in CJP (29.32%). These findings underline the importance of tailored strategies for enhancing WEFE system coordination in urban agglomerations with diverse development gradients. Targeted policy recommendations are proposed based on regional characteristics and subsystem contributions.