Abstract: As a center city in southwest China, Chongqing plays an important role in the national innovation driven development strategy.As the source of scientific and technological innovation, colleges and universities provide innovative talents for the society, which has an important support and protection for the regional innovation oriented economic development. Based on the patent data of 2010-2015 in Chongqing universities and colleges and some famous universities in China, taking statistical analysis and comprehensive evaluation of it by using factor analysis, discussing the problems existed in the scientific and technological innovation ability of universities in Chongqing, proposing the countermeasures and suggestions to improve the scientific and technological innovation ability of universities in Chongqing.