Taking Shuangliu County, Chengdu City, China as an example, evaluation index system for the rights protection effects of farmland transfer contract from three aspects of basic information, transfer agreement and legal safeguards in the contracts. According to the investigation data, weight of evaluation index is determined by both entropy weight and Analytic Hierarchy Process. Comprehensive index method is used to evaluate the rights protection effects of farmland transfer contract in the flat dam, high hill and low hill in Shuangliu County, Chengdu, China. Result shows that the transfer agreement of farmland and the basic information of contract greatly affect the rights protection effects of farmland transfer contract. There are differences in the five indices of the information of the signature of contract, pricing for payment, time limits for farmland transfer, transfer mode of farmland, and use range of farmland transfer. During the farmland transfer in reality, there are three hidden dangers in farmer’s land rights and interests, which are the ill-formed transfer behavior, the relatively low income of farmers from farmland transfer, and the quality decline of farmland and difficult full reclamation in transfer period. Based on the evaluation result and investigation data, countermeasures are put forward to improve the rights protection effects of farmland transfer contract.