Water, energy, and food are indispensable resources for socioeconomic development, and are highly interwoven in urban activities. Clarifying spatial differences in resource consumption is of great significance for coordinated management. However, there is still a lack of a unified assessment for water–energy–food (WEF) nexus flow analysis. This study proposes a comprehensive framework to investigate WEF utilization based on a modified multi-regional input–output (MRIO) analysis. Taking the case of the Yangtze River Delta region, we first inventoried embodied water–energy–food consumption from 2012 to 2017. Then, decoupling analysis and the Logarithmic Mean Divisia Index (LMDI) method were applied to explore decoupling states and identify driving factors. The results show that overall embodied WEF consumption experienced a downward trend from 2012 to 2017, and different provinces varied significantly. Jiangsu had the largest consumption of water and energy, while Anhui contributed a big chunk to food consumption. The manufacturing sector heavily relied on WEF resources and had a great impact on the ecological environment. The decoupling performance indicated a general trend of weak decoupling and strong decoupling in most provinces, with the mining, electricity, and gas supply sectors contributing most to positive decoupling, and the service sectors devoting the most to negative decoupling. As for resource type, water ecological footprint decoupled more than energy and food ecological footprints. Technology level and industrial structure had a major effect on the realization of decoupling, while economic output and population scale were the main restraining factors. Finally, we provide some differentiated policy recommendations for coordinated resource management.