Abstract: The input-output mechanism of science and technology activities has being concerned in China. The judgment mechanism of the efficiency of S&T input-output and the evaluation system of the effectiveness of S&T input-output have been designed in this paper. Based on the main indicators in S&T input and output data during 1995–2015, on one hand, the efficiency of investing in science and technology issues is determined according to the marginal contribution rate of science and technology; on the other hand, the input-output systems of S&T funds and labor power, industry-university-research cooperation funds and labor power, R&D funding sources, and industry-university-research cooperation outputs are uesed as the evaluation systems of the effectiveness of S&T input-output. The results show that since 2003, the efficiency levels of China’s scientific and technological input-output are low, and the effectiveness of S&T input-output shows a positive effect overall.