Based on the background of national urban and rural comprehensive reform pilot area, the introduction of the profiles of research region and the data obtained by on-the-spot interview survey, the innovative models of farmland property rights system reform in Chongqing are introduced by applying participatory rural appraisal methods and examples. The innovative models cover buying shares of contract management rights, transforming from rural residents to urban residents and mortgaging contract management rights. The plights exist in the reform are analyzed, among which the plights of buying shares of contract management rights are introduced from the following five aspects: the conflict with the present land contract laws, the possible new round of massive scale land loses, the confounded functions of government and enterprise caused by risk transference and the difficulties of handling assets when the contract management rights expired. Besides, the plights of the transforming from rural residents to urban residents are analyzed from four aspects, which include the particularity of reform, high financial pressure, emergence of interbedded people and difficulties of payoff of village-based companies. From the facets of limited mortgage area, risks of reimbursing the loan, legal risks of mortgage. The results show that the stock purchasing model of contractual management rights reveals the capital value of land and it is of theoretical and practical significance in law and economics. However, the social security system is not perfect, so the stock purchasing model of contractual management rights can not be expended. In addition, the participation of more famers and the expansion of enterprises are limited. The land comprehensive reform model of transforming from rural residents to urban residents is of positive significance to the comprehensive exploration of farmland property system reform, but this kind of model should based on strong economy. The stock purchasing model of contractual management rights is of significance to perfect the contractual management rights, but it is conflict with the existing laws and financial systems.