Cotton is frequently exposed to high temperatures during the reproductive stage, which can negatively impact productivity. While previous research has shown that photosynthesis can decrease under heat stress, there is limited information on the effects of heat stress during the reproductive phase on crop variables such as radiation capture, use efficiency, and yield. This study aimed to: (i) assess the effect of heat stress on cumulative intercepted PAR radiation (IRcum), radiation use efficiency (RUE), harvest index (HI), and yield, and (ii) evaluate potential interactions between heat stress and source-sink relationships during the reproductive phase. Two field experiments were conducted, with heating treatments applied before and after flowering, and controls without temperature manipulation. In Experiment 1, two genotypes with contrasting growth cycles were compared, while Experiment 2 examined intact versus defoliated plants. Heat stress significantly reduced yield and HI, particularly during post-flowering. Source reduction (defoliation) further reduced yield, independent of temperature. Although IRcum was unaffected by treatments, RUE dropped sharply under heat stress in intact plants and was similarly low in defoliated plants under both control and heated conditions. These results suggest that heat stress, especially during post-flowering, exacerbates the effects on cotton productivity by reducing both total plant dry weight and HI. The study highlights that the relationship between RUE and yield strongly depends on the specific limiting factors, such as heat stress or source restrictions.