In virtue of the integration and interaction perspective to conduct a double-dimensional analysis of the value creation of scientific research institutes, this paper utilized projection pursuit and stochastic frontier model (PP-SFA) method to measure the value creation efficiency of 12 branches of Chinese Academy of Sciences, as well as analyzing its factors. It is indicated that value creation efficiency of the whole Chinese academy of sciences in 2009-2014 is low and its mean is 0.58, which could be improved significantly; The value creation output grows in step with the input of labour and capital, and the disparities between regions was marked in the value creation efficiency; Scientific research institutes of value creation efficiency and application direction and the interdisciplinary research has the positive correlation, and capital source structure has a negative impact on the value creation efficiency of scientific research institutes.