Collaborative innovation of industry-university-institute has put forward higher requirements for talent cultivation， scientific research and the development of social services in universities. It is of great significance to study the relationship between the basic functions and science & technology （S&T） innovation efficiency in universities to stimulate the powerful potential energy of collaborative innovation. Based on the panel data of more than 60 Chinese universities from 2002 to 2016， it applied a two-stage efficiency model to measure S&T innovation efficiency in China. After theoretical analysis， it further empirically analyzed the practical impact of graduate training， strength of ties between universities and industries， research preference and reputation on the efficiency respectively. The main findings are as follows： firstly， the impact of graduate training on S&T innovation efficiency of universities formes an inverted N-type relationship； second， the strength of ties between universities and industries affects S&T innovation efficiency of universities in an inverted U-shaped manner； third， the preference for basic research is conducive to the improvement of S&T innovation efficiency in universities； fourth， academic reputation also has a significantly positive impact on S&T innovation efficiency in universities. It extends the theoretical research on university innovation in the context of industry-university-institute collaborative innovation， and provides important practical inspiration for further exerting the main role of universities.