As a responsible country, China should take on heavy responsibility of energy conservation and emission reduction, and it is an inevitable choice for China to develop high-tech industries and improve the innovation efficiency of high-tech industries in order to alleviate the current environmental pressure. Therefore, this paper takes the panel data of 30 provinces in China from 2005 to 2016 as the research sample, on the basis of using DEA Global-Malmquist index to measure the innovation efficiency of high-tech industries, it constructs three spatial weight matrices, by including spatial geography, spatial economic geography nesting and innovation, and then it uses Spatial Durbin Model to empirically analyze the effect of innovation efficiency of high-tech industry on CO2 emissions in China from spatial perspective. The results indicate: firstly, in China, CO2 emissions gradually increase from 2006 to 2012, however, some provinces have declined after 2012. And CO2 emissions present a descending trend from eastern coastal area to central and western region. Secondly, affected by “warning effect”, CO2 emissions show a significant negative spatial spillover effect. Thirdly, the overall level of innovation efficiency of high-tech industries in China is not high, and its impact on CO2 emissions is not a simple linear relationship, but shows an “inverted N–shaped” curvilinear relation, and its decomposition index EC and TC also have similar characteristics. Obviously, the research in this paper provides a necessary theoretical support for China and some emerging developing countries to rational formulating and effective implementing the energy conservation and emission reduction policies.