China currently suffers from severe environmental issues, particularly with regard to its primary energy consumption. To address the complexity of energy flows, this study integrated a multi-regional input–output method and complex network theory to conduct an in-depth investigation of the functional and structural evolution of energy interaction patterns in the Chinese economy for 2007, 2010, and 2012. Results show that economic scale and trading frequency increased in the regional energy network, while sectoral energy connections remained stable from 2007 to 2012. A time-series analysis demonstrates that Guangdong (R19) was the most vital region for bridging the entire regional energy network and that it was located at the center of energy flow transfers. Sectoral investigation indicates that infrastructure construction remained dominant in the current Chinese economy. Any disruption that occurred in the construction sector may exceed supply capacity, and this would lead to energy crises in the embodied energy flow network. Regions were disaggregated and aggregated during the investigated period because of changes in spatial heterogeneity. Sectoral community analysis explores an evident process for industrial differentiation. The findings of this study provide a new angle through which to understand spatial heterogeneity and industrial structure in a time series manner.