Technological innovation efficiency is measured considering the environmental factors based on three-stage DEA model using Chinese high-tech industries panel data during 2000-2007 and 2008-2014. Our findings are that technological innovation efficiency during 2008-2014 increase significantly compared with 2000-2007. However, technological innovation efficiency is still at a very low level because scale efficiency is too low which is lower than pure technical efficiency. The trend of efficiency change in two periods is consistent after adjusting innovation inputs considering the environmental factors. Technical efficiency and scale efficiency decline, but pure technical efficiency improves significantly. Technological innovation efficiency is quite difference in five first-class industries, the direction of which is inconsistency after innovation inputs are adjusted.