Abstract:The efficiency evaluation on the input and output of state key laboratories has attracted much attention from academics and administration. This paper evaluates the efficiency changes of state key laboratories from 1990 to 2015 based on the information-entropy TOPSIS and DEA-CCR model comparatively. The results show that: by TOPSIS, there is an increase trend in general from the length of distance from the ideal value, meaning that the outputs has risen up quite fast compared with the added inputs; on the opposite, by DEA, the trend is on the downside, which means that there should have been much better outputs because of the rising amount of inputs. On the basis of the above models, four phases of efficiency changes of state key laboratories are proposed, in order to provide a new perspective to evaluate the efficiency of government-funded institutes.