Abstract: Based on statistics data, this paper analyzes the R & D investment and science papers and invention patents of China's colleges, universities and research institutions over the past decade.This paper believes that, China's colleges and universities received a much lower of R & D funds than research institutions, but have acquired a higher innovation efficiency.Compared with the world, our colleges and universities are lower in both the quality and the quantity of their outcomes.The average R & D investment amount per person of CAS is much higher than that of our universities, and their scientific innovation capacity has basically finished the change from the quantity increase to the quality improvement of their scientific papers.For this reason, it is essential for our government to increase the support for universities in R & D investment to make an improvement of their scientific innovation capacity.