This paper evaluates the scientific competitiveness of world-class universities via their research output, with a focus on the position of Chinese universities in the world. Aiming to promote the internationalization of China’s education and scientific research, it observes the development of China’s higher education from an international perspective. This program has been taken for five years during which three reports have been respectively published in 2005, 2007 and 2009. This is the third time to evaluate the world-class universities and research institutions. Original data are obtained from Essential Science Index (ESI) published by Thomson Reuters; subject competitiveness of world universities is evaluated and analyzed in a scientific, subjective and comprehensive way; three categories and thirty pieces of rankings are obtained. The results show that the rankings of most Chinese universities are in the back, revealing that there is still much room for improvement in Chinese universities.