Carbon emissions and carbon flow within a specific area have been studied extensively, but little is known about the effects of inter-regional material and energy exchanges on carbon emissions. In this study, we examined an urban agglomeration in Northeastern China. A carbon emission model was established based on input-output analysis, and robustness analysis was used to test the system’s stability. A new factor for indirect emission dominance intensity was developed to distinguish the significances of indirect emissions and direct emissions. Sectoral control and dependence relationships were explored by ecological network analysis. Results showed that carbon emissions from primary energy consumption were 2.34 times higher than those from secondary energy consumption. The indirect carbon emissions were more than double the direct emissions. The largest direct and indirect carbon emissions come from the advanced manufacturing sector, and the materials and energy conversion sector, respectively. In urban agglomeration, the exploitation relationship between sectors was dominant, suggesting that the structure of the system needs to be improved. Our results provide sector-specific information to help each sector to adjust industrial planning for emission reductions.