Lint yield of upland cotton (Gossypium hirsutum L.) is determined by its component traits, boll number, boll weight, and lint percentage. Selecting high yielding lines is based on the ability to manipulate component traits. In this study, 188 recombinant inbred lines and two parental lines were grown in 1999 and 2000 at Mississippi State University. Lint yield and its three component traits were measured and analyzed by an extended conditional mixed linear model approach. Boll number unit-area −1 made the largest contribution to genotypic and genotype × environment (G × E) variations for lint yield. Both boll number and lint percentage, and boll number and boll weight jointly accounted for more than 70% of the genotypic and G × E variations in lint yield. Ninety-nine percent of the genetic and phenotypic variation in lint yield could be explained by the three component traits, indicating that lint yield was mainly dependent on its three component traits. Small phenotypic variation in lint yield could be accounted for by effects of genotype, G × E interactions of boll number or boll number combined with other component trait(s) ( Table 5). For boll number unit-area −1 a wider distribution of genotypic contribution effects was detected than for lint percentage and boll weight in this study. Boll number and boll weight interacted to affect lint yield, indicating that balanced selection for boll weight and boll number is needed in high-yielding line development. Comparative results with other approaches were also discussed in this study.