Abstract: The good governance for university can be expressed in Chinese way as the modernization of governance system and governance capacity. Under the rapid modernization of national governance system and capacity in China, universities must take the lead in realizing their governance system and capacity modernization. The elements of good governance of universities with Chinese characteristics can be divided into two categories, value-based rationality and instrument-based rationality. By taking the ideal of good governance into the reality, and applying the elements of good governance of universities with Chinese characteristics as indicators, a governance evaluation index system of universities with Chinese characteristics has been constructed here, which includes 7 first-class indicators, 23 second-class ones and 43 third-class ones by using the expert survey method. The advantage of this index system is that it can integrate the value-based rationality and tool-based rationality into university governance, which is helpful to diagnose the modernization degree of Chinese university governance system and capacity, and guides targeted universities to good governance through designed innovative evaluation indexes and standards.