As a new system optimization measure,there is a risk of system performance loss in the “three rights separation”system reform of homestead land， and the property rights governance structure is a key factor that causes system risk. Based on the perspective of property rights governance structure， a theoretical analysis framework for the risk generation of the “three rights separation”system reform of homestead land is constructed from the aspects of property rights arrangement,external environment and subject factors. In the reform practice,the pilot areas of the “three rights separation” system reform of homestead land have formed differentiated property rights governance structure including “weak market and selfguarantee”， “weak market and strong guarantee”，“strong market and selfguarantee” and “strong market and strong guarantee”. However,the uncertainty of the inherent operational mechanism and environmental adaptability deficiencies of the property rights governance structure,results in the potential risks and losses including the difficulty of fully realizing the rights and interests of homestead land,insufficient benefits of the reallocation and reuse of homestead land. In order to prevent and control the risks of the “three rights separation” system reform of homestead land,the specific measures of risk control should be formulated from two aspects:firstly,improve the transaction system and supporting measures,and enhance the efficiency of homestead property rights governance structure; secondly,strengthen the main position of farmers,promote reforms according to local conditions,and improve the adaptability of the property rights governance structure.