Improving the energy efficiency is a fundamental way to ensure energy security and sustainable development, and is also the requirement of supply-side structural reform of China’s energy. This paper uses the DEA-BCC model to estimate China’s energy efficiency at the provincial level, analyzes its regional differences from 2006 to 2016, and applies a panel data model to analyze the influencing factors of energy efficiency. It selects labor, capital stock and total energy consumption as inputs and takes real GDP and comprehensive index of environmental pollution as desirable and undesirable outputs, respectively. The results show that (1) energy efficiency when undesirable output is included is generally lower than when undesirable output is excluded; (2) There is a considerable difference in energy efficiency among provinces, and China’s energy efficiency, by and large, shows a trend of declining. The energy efficiency of four major regions demonstrates obvious regional differences: coastal region>northeastern region> middle region >western region; (3) The economic development level, technological progress, energy price and urbanization level are positively associated with energy efficiency, while the proportion of secondary industry and the energy consumption structure dominated by coal and oil are negatively correlated with energy efficiency.