Technical Abstract: Dissection of the genetic relationship between lint yield and its yield components at the chromosome level may provide an additional avenue for yield enhancement in cotton (Gossypium hirsutum L.). Based on the conditional additive-dominance (AD) genetic model, we investigated the genetic structures of lint yield with its three component traits, lint percentage, boll weight, and boll number, using a two-location data set containing cotton chromosome substitution lines (chromosome or chromosome arm substituted from G. barbadense L. into G. hirsutum L., TM-1) which are defined as CS-B lines and their F2 hybrids with CS-B recurrent parent TM-1. We calculated the conditional variance components, contribution ratios, and contribution effects subject to the additive and dominant components. Our results showed that boll number or boll number greatly reduced the conditional variance components and phenotypic variance for lint yield and thus indicated that boll number plays a more important role in lint yield than the other two component traits. We demonstrated that the G. barbadense chromosomes in CS-B16, CS-B18, and CS-B4sh were directly associated with reduced lint yield. Substituted chromosome arms 14sh, 22sh, and 22Lo were associated with reduced additive effects for lint yield through the component of boll weight, thus suggesting that some substituted chromosomes or chromosome arms may be indirectly associated with lint yield through yield component traits. This study provides a better understanding of cotton yield and its component traits at the chromosome level and this information should be useful in cotton breeding.