Abstract: Cotton cultivar NuCOTN 33B was planted in isolated pools treated with drought or waterlogging for 7 or 14 d to explore their effects on cotton boll carbohydrate content and its relationship with the biomass accumulation. The results showed that the drought treatment reduced the carbohydrate content of cotton boll shell on middle fruit branches, but had a weak effect on cotton boll shells on lower fruit branches. Soluble sugar, starch and sucrose contents of cotton boll shell on upper fruit branches under the drought condition and on whole plant branches under  waterlogging treatment changed similarly, namely, the soluble sugar and starch content increased, while the sucrose content went down firstly and then increased later, which indicated that the exportation of sucrose from boll shell was inhibited and became worse with the increase of waterlogging duration. Compared with the boll shell, the carbohydrate contents of cotton seed were less affected by the drought and waterlogging treatments at the flowering and bolling stage. Under the treatments of drought and 7 dwaterlogging, the biomass accumulation of cotton bolls on the middle fruit branches initiated earlier but lasted less days, and the maximum speed at lower and upper fruit branches reduced, while the treatment of waterlogging for 14 d caused the decline of maximum speed of biomass accumulation of bolls on whole branches. On the other side, the correlation analysis showed the significant positive relationships among the boll biomass, the maximum speed and the contents of soluble sugar and sucrose in the boll shell respectively. In conclusion, the treatment of drought and waterlogging at the flowering and bolling stage retarded the outward transportation of sucrose from cotton bolls, changed the boll biomass accumulation characteristics, and therefore were detected as the important cause of cotton boll total biomass reduction.