Abstract Regional disparity in terms of industrial energy efficiency is noticeable in China due to the unbalanced economic progress in past decades. Analyzing the provincial industrial energy efficiency and its influencing factors is of great significance to formulate differentiated policies. To date, the influence of many social-economic factors on the industrial energy efficiency have been examined but the impact of the inter-industry structure has almost been ignored. In this paper, the slacks-based measure model incorporating undesirable output is applied to evaluate the industrial energy efficiency both at the provincial level and the sectoral level in China for the period 2010 to 2016. Then, industrial structure efficiency is introduced, which reflects the inter-industry structure and takes the sectoral-level energy efficiency into consideration. And the impact of the industrial structure efficiency on provincial industrial energy efficiency is tested by Tobit regression model. The results show that huge discrepancies of provincial industrial energy efficiency exist and the industrial structure efficiency is confirmed to be a determinative factor to the provincial industrial energy efficiency, with the coefficient of 0.525. Policy recommendations are provided for adjusting the provincial inter-industry structure and improving the industrial energy efficiency.