Abstract: This paper analyses the transformation of S&T achievements in Chinese college and universities from the aspect of knowledge flow and dose a comparison with American colleges and universities. The results are firstly, in overall, the transformation in Chinese colleges and universities are better than American colleges and universities. Secondly, the patent transformation and application in Chinese colleges and universities are lower and the imbalanced structure of knowledge flow is the main problem of Chinese colleges and universities. This paper analyses the reasons for this phenomenon and gives relative suggestions.