By adopting an energy-input based directional distance function, we calculated the shadow price of four types of energy (i.e., coal, oil, gas and electricity) among 30 areas in China from 1998 to 2012. Moreover, a macro-energy efficiency index in China was estimated and divided into intra-provincial technical efficiency, allocation efficiency of energy input structure and inter-provincial energy allocation efficiency. It shows that total energy efficiency has decreased in recent years, where intra-provincial energy technical efficiency drops markedly and extensive mode of energy consumption rises. However, energy structure and allocation improves slowly. Meanwhile, lacking an integrated energy market leads to the loss of energy efficiency. Further improvement of market allocation and structure adjustment play a pivotal role in the increase of energy efficiency.