Chinas public institution is a kind of special public service organization, so its performance evaluation should be an importance element of evaluating objects of public sector. Now, due to inefficient management and over-marketing of public institution, public institution performance evaluation is overlooked relatively in Chinese public sector performance evaluation, while government performance evaluation is over stressed. This paper discusses the basic dimension and theoretical principle of building index system of public institution performance evaluation from the angle of governance structure of Chinas public institution, which is beneficial to building a scientific index system to improve public institutions performance and to perfect the governance structure.