In this paper, we set up an index system of input and output of scientific research in colleges and universities. We use factor analysis to extract common factors from input and output indicators respectively. Based on this, the paper focused on the input-output efficiency of science and technology in colleges and universities in Henan Province and its changing trend where BC2 model is used. The results showed that in 2006 and 2011-2015, the comprehensive efficiency and technology Efficiency and economies of scale are both valid and above the national average. 2007-2009 did not reach DEA in terms of technical efficiency and economies of scale. In 2010, they were technically efficient but inefficient in scale and below the national average. The result shows that main reason for the decrease in efficiency lies in the lack of input into the exchange of personnel and the number of papers exchanged in international conferences. In this regard, the reletive policy proposals of Henan universities to maintain and increase the input-output efficiency of science and technology are put forward.