The innovation achievements are decomposed into academic output and economic output from the perspective of innovation types, then this paper performs the exploratory research on the aspects of academic output efficiency, economic output efficiency and key influencing factors by using SFA method. The primary findings of the study can be summarized as follows: Firstly, the academic output is an investment-driven innovation activity, and the growth of academic output relies principally on the investment of R&D expenditure. R&D expenditure has a negative influence on economic output efficiency, while the appropriate increase of R&D personnel could help to improve the efficiency of economic output. Secondly, academic output efficiency and economic output efficiency is significantly different among colleges located in different provinces, but they distribute in rundle: the east is the highest, followed by the middle, the west is the lowest. The results show that there is a certain degree of association between the S&T innovation efficiency of colleges and local economic development level. Thirdly, the existing appraisal mechanism stressing on quantity results in the significantly negative correlation between the quality of R&D personnel quality and the academic output efficiency, while the non-significant negative correlation between R&D personnel quality and economic output efficiency. During the sample period, the increase of the government's support for S&T innovation activities in colleges cannot effectively improve the academic output efficiency.