The mortgage of property rights of farmer housing in China has its specific connotation. The perfection of mortgage loan of property right of farmer housing is the key element to solve the issues of agriculture, farmers and rural areas. Because of the serious legal defects of the current system of mortgage of property rights of farmer housing as well as the imperfection of the market of mortgage of property right of farmer housing and risk mitigation mechanism, the mortgage loan of property rights of farmer housing has faced difficulties during the process of implementing. The way to perfect the system of mortgage of property rights of farmer housing is as follows: reconstituting the rule of mortgage of property rights of farmer housing; perfecting the market of mortgage of property rights of farmer housing by improving system of mortgage registration, price evaluation system and trading market; perfecting the risk mitigation mechanism by establishing multiple guarantee mechanism, creating government risk funds and perfecting of social security system.