In response to climate change and to achieve global sustainable development, countries should accelerate the transition of their energy systems. In order to clearly understand the underlying mechanism of the transition, it is necessary to investigate the structural changes along energy flow processes and find the driving factors. This paper proposes a quantitative method based on energy allocation Sankey diagrams and index including total amount change, relative growth rate and occupation ratio change (TRO) to evaluate the structural changes of energy flow process and presents a case study of China from 2005 to 2015. Firstly, China’s energy flow process in 2015 was mapped from energy sources, intermediate conversion, end-use devices, passive systems to final services in the form of a Sankey diagram. Secondly, based on TRO index, this diagram was compared with a previous one of 2005 to reveal and evaluate structural changes in the past decade. Finally, the driving factors of these changes were discussed from different perspectives. The main changes from energy sources level are the reduction of coal and the increase of natural gas, from final services level are the reduction of thermal comfort demand and the increase of structural materials (especially that from chemical industry). The key factors driving these changes are the infrastructure construction of natural gas, rapid urbanization, improvement of energy efficiency of buildings and the people’s pursuit of high-quality life.