After evaluating the S&T output based on the TOPSIS, this paper obtains the only output variable and analyzes the interaction between the S&T input and output based on the panel data and the panel vector auto-regression model. The results show the obvious interaction between the input and output in Chinese universities, which forms a benign positive feedback effect. There exist bidirectional granger causalities among the scientific research funds, the research and development staff full-time equivalent and the scientific research output. The scientific research personnel number is the granger cause of scientific research output, and the research output is the granger cause of the scientific research personnel number only in the next lag stage. Whether the impulse response function or the variance decomposition, each variable except for itself is the biggest influence to the scientific research output, indicating that there is a great interaction between the scientific research output and the input. The scientific and technical personnel number makes the largest contribution to the scientific and technical output, the research and development personnel full-time equivalent is the second contribution and the scientific research funds is the third. Finally, this paper analyzes the reason for such contributions.