This paper uses the method of Data Envelopment Analysis (DEA) to make an empirical analysis on the 14 industry’s Industry-Study-Research Comprehensive Efficiency which the government has invested a lot. Through the analysis found that on the whole our country’s Industry-study-research Comprehensive Efficiency is relatively good, but some industries did not achieve the optimal allocation of resources, the efficiency of scientific research still needs to be improved. Therefore, the government should strengthen the guidance, enterprises should cooperate with colleges and universities actively to promote the long-term healthy development of the industry.