As an energy- intensity sector, the industrial sector consumes 70% of energy and generates more than 50% of CO_2 in China. According to data spanning 36 industrial sub- sectors from 2006 to 2012, we adopted a non- radial DEA model which combined Natural Disposability and Managerial Disposability to study energy and environmental unified efficiency. Input indicators including fixed assets, energy and labor were considered as inputs under Natural Disposability, and R&D investment was regarded as an input under Managerial Disposability. The government promotes R&D investment on energy- saving technology and equipment in the industrial sector in Chinas National Plan on Climate Change. This study also verified whether R&D investment was effective for different industrial sub- sectors to reduce undesirable outputs based on DEA modeling. Truncated regression modeling was adopted to analyze factors driving energy and environmental unified efficiency. We found that thirty-two sub-sectors had great room to improve their energy and environmental performance except for four sub- sectors (e.g. tobacco products industry). The unified efficiency scores of three sub-sectors including the coal mining and washing industry, chemical raw materials and chemical products manufacturing industry and nonmetallic mineral products industry were all below 0.8, while the non-metallic mineral industry was 0.472 in this case. In 2012, R&D investment was effective for 16 sectors including coal mining and washing industry. Energy mix, technological innovation and market competition had significant impacts on unified efficiency. The proportion of coal consumption had a negative influence on unified efficiency, and the relationship between the ratio of R&D investments and unified efficiency was positive.