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Background:Photosynthate partitioning and within-plant boll distribution play an important role in yield formation of cotton;however, if and how they interact to mediate yield remains unclear. The objective of this study was to investigate the genotypic variance in photosynthate partitioning and within-plant boll distribution, with a focus on their interactions with regard to yield and yield components. A field experiment was conducted in the Yellow River region in China in 2017 and 2018 using a randomized complete block design with three replicates. Photosynthate partitioning of three commercial cultivars (DP 99B, Lumianyan 21 and Jimian 169), varying in yield potential, to different organs (including bolls) at early flowering, peak flowering, and peak boll-setting stages, as well as within-plant boll distribution at harvest, and their effects on yield formation were examined. Results:Lint yield of Jimian 169 was the highest, followed by Lumianyan 21 and DP 99B. Similar differences were observed in the number of inner bolls and boll weight among the three cultivars. J169 partitioned significantly more photosynthate to the fruit and fiber than Lumianyan 21 and DP 99B and allocated over 80％of assimilates to the inner bolls. Additionally, Lumianyan 21 allocated a higher proportion of photosynthate to bolls and fiber, with 12.5％-17.6％more assimilates observed in the inner bolls, than DP 99B. Conclusions:Genotypic variance in lint yield can be attributed to differences in the number of inner bolls and boll weight, which are affected by photosynthate partitioning. Therefore, the partitioning of photosynthate to fiber and inner bolls can be used as an important reference for cotton breeding and cultivation.