Abstract: Due to the lack of scientific evidence and methodology for selection of sites for High Quality Capital Farmland Construction Project (HQCFCP), this research focused mainly on exploring and evaluating methods of HQCFCP site selection. Based on the understanding of the principles of set pair analysis (SPA), Liangping County of Chongqing City was selected as a case study research area. According to the malleability of the original relations and through improvement of the analysis method by extending the three-level justification into four-level, and integrating the entropy method with set pair analysis, an evaluation on the reasonability of site selection was finally conducted for the implementation of 14 HQCFCPs in 2014. The SPA and en-tropy method composed of the construction of evaluation index system and classification standard along with the calculation of entropy indices and connections as well as the determination of evaluation levels. Also in order to verify the feasibility and reasonability of SPA, the SPA conclusions were compared with conclusions from fuzzy synthetic evaluation (FSE). The results showed that the sites selection of HQCFCPs in Liangping County was largely reasonable. Specifically, based on the level of justification standard, the sites selection for HQCFCPs at Shuanggui Village of Jindai Town was classified as reasonable. Only two villages (Leying Village of Yinping Town and Tiangu Village of Liangshan Town) had moderate unreasonability for HQCFCPs sites selection. Sites selection for HQCFCPs construction on the rest of the 11 projects areas were all evaluated as moderately reasonable. The influencing factors of site selection reasonability for HQCFCPs mainly included the depth of top soil layer, soil organic matter content, density of water system and the rate of guaranteed irrigation. The SPA results were basically similar to FSE results. In some project areas, the results seem to be different, although no inconsistency was noted. The application of SPA evaluation method yielded more information and was more beneficial to displaying the diversity of various evaluation units. Moreover, the results were more accurate and reliable and the method was therefore practicable and valuable. This study provided the scientific evidence for the selection of sites for HQCFCPs establishment in Liangping County. It also provided the needed information on the reasonability of site selection by using scientifically feasible method.