Because of the importance of universities to the national innovation system, the evaluation of university innovation capabilities currently is a hot spot in the field of scientific evaluation. Based on the “Innovation Index of China Univ. in 2012” issued by RCCSE, this paper uses its indicator data to do a deep analyzis on the university innovation capability. It firstly analyses university types and province distribution. Then it applies multiple linear regression model to investigate the relationships between “Overall Rank” and “Input Rank” “Output Rank” and “Benifit Rank”. Also, it does some analysis on ordinary universities entering “Top 100 Innovation Index of China Univ. in 2012”. Finally, some conclusions and discussions are given.