As external balancing mechanism，third-party evaluation has the advantage of independence，objectivity and impartiality，compared with internal evaluation. Independence is the core of evaluation，which is critical to objectivity and impartiality of evaluation finding. In this study, the comparison had been on third-party evaluation, independence evaluation and external evaluation，which had different emphasis. The third-party evaluation focused the evaluators, which aimed to differ with the fist party and the second party. Modern Agriculture Industrial Technogical System (MAITS) is a program, which have been funded by Ministry of Agriculture (MOA) in China for almost 8 years. In order to account to public，the third-party evaluation was asked to do on MAITS in 2015. This study took this evaluation as an example, and discussed what was third-party evaluation's independence. In this case study, independence needed to be ensured from two parts, evaluation organizations and evaluation procedures. Fisrtly, independence of evaluators contained spirit, institutions and their members, and legal status of institutions. Secondly, independence of evaluation procedures was suggested to ensure through both itself and external. As for procedures, three points needed to be involved, including choosing experts, getting data, and forming the evaluation report. As for the external supervision, there were four pionts including introducing competition mechanism, disclosuring the evaluation process and results, constructing an open and transparent supervision mechnism, and improving the use of results.