Abiotic stress, particularly heat stress, affects various parts of the cotton plant and ultimately impacts the seed cotton yield. Different portions of a single cotton plant of a cultivar exhibit variable responses to stress during reproductive and vegetative phases. To test this hypothesis, physiological and morphological traits related to heat stress were observed for two flowering positions in 13 genotypes of upland cotton. These genotypes were sown in field conditions in triplicate following a randomized complete block design. Data were collected for pollen germination, pollen viability, cell membrane thermostability, chlorophyll content, boll weight, and boll retention for both the top and bottom branches of each genotype. The collected data were analyzed for the identification of variability within and between genotypes for these two flowering positions. Tukey’s test was applied to estimate the significance of differences between genotypes and positions within each genotype. Results showed that the two positions within the same plant statistically varied from each other. The bottom branches of the genotypes performed significantly better for all traits measured except boll weight. The genotype AA-933 performed best for pollen germination and boll retention, while CYTO-608 exhibited maximum pollen viability in both the bottom and top flower positions compared with other genotypes. Overall, MNH-1016 and CIM-602 showed better cell membrane thermostability and chlorophyll content, respectively. This intra-plant variability can be further exploited in breeding programs to enhance the stress tolerance capabilities of the resulting varieties.