Abstract: A national scheme of "Three land spaces and three control lines" has been one of the most important strategies for land spatial planning and land policy in China. It is a high demand to delimitate the boundaries, and then implement the strategy of functional zones, particularly for the new pattern in the territorial space. In this study, a technical route and optimization principles were proposed for the permanent basic farmland layout using the overall delimitation of the "three land spaces and three control lines". The "three land spaces and three control lines" were also efficiently delineated, in order to deal with the disunity of the base map, inconsistency, and crossing of the boundary. The Third National Land Resource Survey data and the production-ecology-landscape indicators of comprehensive quality evaluation were constructed for the permanent basic farmland. Specifically, the comprehensive quality evaluation indicators were selected using the production condition, ecological condition, and location condition of cultivated land, which were the three primary indicators. Each primary indicator included several secondary indicators, including cropland quality, planting suitability, ecological protection importance, ecological regionalization, water environment risk, and cropland contiguity. Each indicator was assigned as several classification threshold values and weights, in order to evaluate and score the cultivated land parcal. More importantly, the water environment risk was selected as the indicator, considering the risk of water pollution from the non-point source of cultivated land. A case study was finally selected in Meihekou City, Jilin Province, China. The results showed that: 1) The specific area of optimized permanent basic farmland was 91 680.82 hm2 with an increase of 1 290.69 hm2. The area of cultivated land quality at level 10 increased by 3 523.99 hm2, and that of level 12 decreased by 2 324.85 hm2. The average area of permanent basic farmland patches increased from 1.91 hm2 to 2.61 hm2. The area and quality of permanent basic farmland were improved after optimization, indicating a much more stable layout in the study area. 2) Among them, the permanent basic farmland of 20.74 hm2 remained within the ecological red lines as the permanent basic farmland. In addition, the overlapped area was deleted from the ecological red lines. There was also the permanent basic farmland of 1 388.47 hm2 within the urban development boundary, which was removed from the permanent basic farmland, due to its low quality. The high-quality permanent basic farmland was still reserved within the urban development boundary, whereas, the overlapped area was removed from the urban development boundary, indicating the spatially consistent three lines. Food security, ecological protection, and urban development were considered in this case. The spatial layout of agriculture, ecology, and town space was optimized with coordination. The finding can provide a strong reference for the decision-making on the "three land spaces and three control lines" delimitation and land spatial planning.