Based on the related data of scientific and technological input and output in 2011—2015 years,Grey relational analysis and L-Q grey prediction model are adopted,This paper makes an association analysis and prediction of 8 inputs and outputs of science and technology in 38 provincial public welfare research institutes in Fujian. The results show that there is a strong correlation between scientific and technological input and output, and the increase of scientific and technological input can effectively improve the level of scientific and technological output; At present, different input of science and technology has different effects on different outputs, But in the next 5 years, The working efficiency and innovation ability of scientific and technical personnel will become the important factor to decide the efficiency of scientific research output. Therefore, in order to improve the efficiency of science and technology input and output, we must attach great importance to talent training and optimize the talent structure, while continuing to increase the material input of science and technology funds.