Drought appears at flowering and boll formation for cotton frequently. However, reports on the impact of carbon dynamics in the subtending leaf on boll biomass under periodic droughts are limited. To investigate this, experiments were carried out with two cultivars (drought‐tolerant: Dexiamian 1; drought‐sensitive: Yuzaomian 9110), three water levels [soil relative water content (SRWC): control (75 ± 5)%, moderate drought (60 ± 5)%, severe drought (45 ± 5)%] and five drought durations (10, 17, 24, 31 and 38 days). A 38‐day drought declined the net photosynthetic rate of subtending leaf, which could be collectively attributed to the reduction in carboxylation with reduced ribulose‐1,5‐bisphosphate carboxylase activity, and stomal limitation with decreased stomatal conductance, along with the damage of photosynthetic apparatus with depressed maximum and actual photochemical quantum yield, leading to lower starch content. A 38‐day drought also increased the activities of sucrose phosphate synthase (SPS), sucrose synthase (Susy) and expressions of genes (GhSPS1, GhSPS2, GhSusA and GhSusB) associated with these enzymes, causing the accumulation of sucrose content, finally resulting in lower boll biomass. Some of the above parameters fully recovered under more than 17‐day moderate drought or over 10‐day severe drought, but boll biomass still decreased after re‐watering. Under 10‐day moderate drought, all aforementioned indices and boll biomass were completely recovered within 7 days of re‐watering, and the recovery capacity of Yuzaomian 9110 was lower than that of Dexiamian 1. Therefore, rapid recovery of photosynthesis and decline in the subtending leaf sucrose content to pre‐stress levels are important factors in lessening the impacts of drought on boll biomass and are indicative of cultivar tolerance to short‐term moderate water deficit.