There is no consensus on whether state-owned enterprises (SOEs) or privately-owned enterprises (POEs) pollute more. This study explores the impact of ownership on pollution emission intensity using micro-data from Chinese industrial enterprises. From the perspective of energy efficiency, the mechanism of ownership affecting pollution emissions is explored further. Research results show that the pollution emission intensity of SOEs is significantly higher than that of POEs. The underlying reason is the low energy efficiency of SOEs, and energy efficiency plays an important mediating role in the relationship between ownership and pollution emissions. Among industrial waste gas, nitrogen oxides (NOx) and dust emissions, energy efficiency plays the largest mediating effect between ownership and NOx emissions. Additionally, in both high-polluting and low-polluting industries, SOEs’ pollutant emission intensity is higher than that of POEs, however, the mediation effect of energy efficiency is greater in low-polluting industries. In cities with high growth pressure, SOEs’ pollutant emission intensity is more significant than that of POEs. On the contrary, there are no noticeable differences in pollutant emission intensity between SOEs and POEs in cities with low growth pressure. But the mediation effect of energy efficiency is more significant in cities with high growth pressure. Industrial enterprises are the ultimate sources of industrial pollution. Therefore, the formulation of effective environmental policies cannot be separated from the analysis of enterprises’ emission behaviors and the assessment of micro factors affecting emissions. The conclusions of this study provide a basis for developing countries to formulate environmental policies for industrial enterprises.