Based on the data collected by the Center for Private Enterprises Studies of CASS in 2007，this paper analyzed empirically the key factors of the human capital of the entrepreneurs in Non-Governmental enterprises on the selection and innovation of the institutions in corporation governance in the approach of Ordered Logistic Regression. This paper concluded that with the more entrepreneurial human capital accumulated；the Non-governmental entrepreneurs were more likely to adopt the modern corporation institutions. The accumulation of the managing experiences and leadership of the Non-Governmental entrepreneurs were very important to the selection and innovation of the institutions in corporation governance. In Non-Governmental enterprises，the separation between the owners and managers would make the owner take some measures in the property rights to control the managers. The CPC membership of the founder of the Non-Governmental entrepreneurs was a key factor on the selection and innovation of the institutions in corporation governance.