In this paper, multi-regional input–output analysis (MRIO) and ecological network analysis (ENA) are combined to assess carbon flows within China and identify key regions and sectors in the context of spatial heterogeneity for effective carbon mitigation. An interregional carbon network model is established by articulating the directions and magnitudes of carbon flows based on MRIO. ENA is then used to unveil indirect carbon flows and mutual relationships among regions. The results show that the northwest is the largest controller for most regions in China. Most carbon emissions in the rest of China are induced by the east’s final demand and substantial consumption. In addition, at sectoral level, the control and dependence abilities vary by region in China. This study provides an integrated framework to investigate interregional carbon emission structure, identify efficient pathways for coordinated emission mitigation, and reduce global carbon inequality across regions.