Urban energy metabolism includes processes for exploiting, transforming, and consuming energy, as well as processes for recycling by-products and wastes. Embodied energy is the energy consumed during all of these activities, both directly and indirectly. Multiregional input-output (MRIO) analysis can calculate the energy consumption embodied in flows among sectors for multiple cities or regions. Our goal was to address a problem apparent in previous research, which was insufficient attention to indirect energy flows. We combined MRIO analysis with ecological network analysis to calculate the embodied energy consumption and the energy-related carbon footprints of five sectors in three regions that comprise the Jing-Jin-Ji agglomeration, using data from 2002 and 2007. Our analysis traced metabolic processes of sectors from the perspective of final consumption. Based on the embodied energy analysis, we quantified the indirect energy consumption implied in exchanges of sectors and its distribution and identified the relationships formed through the indirect consumption to analyze the roles of providers and receivers in the system. Results showed that the embodied energy consumption for the Jing-Jin-Ji region increased from 2002 to 2007 as a result of increased energy consumption in Tianjin and Hebei. Overall, consumption of Beijing decreased likely attributable to the fact that government policies relocated industries during this time in anticipation of the Olympic Games. The relationships among sectors changed: Beijing changed from a net exporter to an importer, whereas Hebei changed from a net importer of energy from Beijing to an exporter to Beijing, and Tianjin served as an importer in both years.