The farmland quality in the peripheries of Beijing, Shanghai, Guangzhou, Chongqing and other 14 major cities is to be designated as permanent prime farmland according to the requirement of the Ministry of Land and Resources and the Ministry of Agriculture in 2014. Demarcating the permanent prime farmland scientifically is of great significance. In this paper, Beibei District of Chongqing City was taken as the study area, the index systems of comprehensive evaluation of farmland quality and of the site condition of farmland were constructed with in LESA system and ArcGIS10.2 platform. Local autocorrelation analysis of farmland was used to identify the key protected area, and the prime farmland plots were selected after comparing the results of LESA evaluation and of local spatial autocorrelation analysis. The results indicated that farmlands could be divided into priority area, encouragement area, reserve resources area and inappropriate area. The priority area, the encouragement area and a part of the reserve resources area could be designed as the permanent prime farmland area with an area of 2 310.9 hm², accounting for 21.13% of the total farmland area, and with an average evaluation score of 64.47, indicating better quality and stability. The area of newly-designed prime farmland was 9.94 hm² more than that of the original prime farmland, and the area of the advantaged farmland was 2 111.79 hm² more than the original prime farmland at the same level. The new method can capture the characteristics of farmland, and quantitatively analyze the quality characteristics, the site conditions and the spatial agglomeration characteristics of farmland, greatly improve the quality, stability and spatial agglomeration of farmland than before, thus is more helpful to protect the high quality farmland, boost city transformational development and improve urban ecological environment.