Abstract The energy supply–demand security and climate change has continued to be problematic, making it significant and necessary to investigate embodied energy flow, particularly in a large and fast-growing developing country like China. One of the effective approaches is the energy/emissions embodied in bilateral trade (EEBT) aiming to locate the destination of energy bi-directionally to evaluate how energy flow between producer and consumer sectors. However, in addition to the flow of energy and resources, the topological structure and impact of underlying components from a system science perspective are equally important for policy-making. This study therefore constructs an energy embodied in trade network (EETN) model to track multi-layer primary energy flow by integrating the EEBT approach and complex network analysis. The embodied coal, oil, natural gas, and non-fossil fuels associated with China’s 30 provinces/municipalities are quantified at the provincial level. By the joint analysis of the network-oriented metrics, the EETN model elicits the possibility of understanding the heterogeneity distribution of different types of energy flow and the potential impact of province-specific policy interventions. We explain how resource endowment, economic growth, income inequality, cross-provincial industrial transfer, and infrastructures affect China’s provincial energy embodiments as well as the clustering features. Other findings and policy recommendations are also presented.