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Cotton seed production is the main form of agriculture in Xinjiang, China. Unreasonable distribution of cotton seed production results in a waste of water, land, and human resources. In this study, we established a hierarchical classification integrating method; investigated the spatial suitability of climate, land and water resources, and infrastructure; examined the production risk and planting history; and integrated spatial suitability and production risk and history to produce the spatial layout of seed production for early-maturing cotton (EMC), early–medium-maturing cotton (EMMC), and long staple cotton (LSC) in Xinjiang. The results indicated that the appropriate areas for EMC, EMMC, and LSC seed production are 6.4 × 10⁵, 5.5 × 10⁵, and 3.6 × 10⁵ ha, respectively. By combining the suitable areas of seed production for the three cotton species, we concluded that the superior and most suitable area for producing cotton seed of EMC, EMMC, or LSC is located in the western Tarim Basin. The sub-suitable area for cotton seed production of EMC, EMMC, or LSC is mostly distributed in the western and northern Tarim Basin. This research provides a good solution to the selection of cotton seed production base; however, adoption will depend on the actual preference and market factors.