Abstract:The efficiency of input and output of scientific research in our country are in urgent need of ascension, along with the “Thirteenth plan of five-year national development”, the problems blocking the development need be solved, so the colleges and universities are chosen as the research object for they are regarded as the national science and technology innovation powerhouse. The input and output of scientific research in colleges and universities data sorting analysis is connected with the method of grey correlation analysis and Perason correlation coefficient test, the research is focused on the main factors influencing the efficiency of input and output of scientific research in colleges and universities, on this basis, certain corresponding measures are put forward, including paradigm innovation, product and service innovation, orientation innovation, process innovation and mechanism innovation.