Based on the basic research, applied research and experimental development data of Chinese universities' scientific research from 2006 to 2015, the paper measured the total factor productivity(TFP) of the above three scientific activities with the method of DEA-Malmquist index , and analyzed according to their fluctuations. This search showed that ,first, the TFP of basic research showed a downward trend, and the TFP of applied research and experimental development showed an upward trend; second, the technical change is the major factor affecting the TFP of the three scientific research activities, and more than 50% of Chinese provinces cannot effectively and comprehensively improve the TFP of the three scientific research activities .Third, based on the data, dividing the distribution of China's scientific research capabilities into "the first class area", "the second class area ", "the third class area ", and "the fourth class area ". Countermeasures and suggestions was proposed according to the conclusions drawn from this paper.