Abstract The leaf subtending to a cotton boll (LSCB) is vital to boll development and biomass, but few studies have examined the effects of drought on the source capacity of LSCBs on different fruiting branches (FBs). To investigate the response of LSCB photosynthesis on different FBs and the relationship of boll biomass to drought, a drought experiment was performed with three treatments: well‐watered (WW, soil water relative content [SRWC] 75 ± 5%), mild drought (MD, SRWC 60 ± 5%), and severe drought (SD, SRWC 45 ± 5%). Despite photosynthetic active radiation increasing under drought conditions, the pre‐dawn leaf water potential, net photosynthesis rate ( Pn ), stomatal conductance ( Gs ), transpiration rate ( Tr ), and maximum quantum yield in PSII (Fv/Fm) under MD and SD significantly decreased when compared with WW, with a more pronounced decrease observed on upper FBs. Additionally, the maximum sucrose and hexose levels in LSCBs increased under drought conditions, whereas the maximum starch content decreased on FB 10–11 , but showed a varied trend on FB 2–3 and FB 6–7 . Although carbohydrate levels in the LSCBs increased, biomass per cotton boll decreased. More importantly, the ratio of cotton boll biomass was significantly correlated to the maximum sucrose content ratio on each FB, indicating that sucrose allocation was important to cotton boll biomass. Cotton boll biomass notably decreased on upper FBs, but was maintained on lower FBs, indicating that drought promoted carbon allocation in older bolls. Thus, LSCBs and cotton bolls on upper FBs were more affected under drought conditions due to decreased photosynthesis and carbohydrate allocation.