Leaf is one of the main photosynthetic organs, while other green parts of plant also retain or develop chlorophyll and have photosynthesis. To better understand the whole plant photosynthesis production potential and contribution to cotton yield, we selected Xinluzao 33 and Xinluzao 45 (two common cultivars in Northern Xinjiang) with three irrigation treatments (CI, conven- tional irrigation; SDI, slight deficit irrigation; MDI, moderate deficit irrigation) to measure the chlorophyll content (Chl), net pho- tosynthetic rate (Pn), stomatal conductance (gs) and photosynthate accumulation in leaf and non-leaf green organs during different growth stages and the contribution of non-leaf green organs to yield. The results showed that the Pn and Chl in non-leaf organs were relatively insensitive to soil moisture stress, decreasing by only a small amount between 25 and 45 days after anthesis. With reduction of water supply, the dry matter production in non-leaf green organs played more important roles in cotton yield forma- tion. Cotton boll weight in the moderate deficit irrigation treatment decreased by 16.8% to 34.9% when the bolls (capsule walls plus bracts) were shaded and by 7.6% to 17.5% when the stalks were shaded. Hence, limiting-irrigation treatment is important to maintain high leaf photosynthetic rates. It is also important to develop the potential photosynthetic capacity of non-leaf green or- gans. This is especially important when leaf photosynthesis capacity declines due to leaf aging or water stress.