Water deficiency has a serious effect on cotton productivity. Development of cotton bolls determines cotton fibre yield and quality and is affected by many environmental variables, including water availability. However, we know little about the effect of water stress on boll development and the final fibre yield and quality of the varieties with different boll sizes. In this study, cotton varieties with different boll sizes were used to compare the effect of water availability on boll development, characteristics of fibre yield and quality, seed components and seed vigour. The results showed that under the well-watered (WW) and water-deficit (WD) irrigation conditions, large boll (LB) and small boll (SB) varieties had a similar overall trend of boll volume change and accumulation of boll dry matter during boll development, but differed in the rate of dry matter accumulation and boll volume growth. Under WW treatment, the dry matter accumulation per boll of LB was significantly higher than that of SB at 42 days postanthesis (DPA), with a difference of 29.17%. WD led to a reduction in dry matter accumulation of bolls, and the dry matter accumulation in seed cotton and boll shell for LB varieties decreased by 20.45% and 3.24%, respectively, at 42 DPA. The corresponding decrease in SB varieties was, respectively, 16.76% and 2.81%, but the harvestable boll numbers per plant of SB varieties were 36.28% higher than that of LB varieties under WD irrigation. The lint yield of the SB varieties was 1042.45 kgha(-1) and the seed cotton yield was 2459.67 kgha(-1), which were also comparable to those of the LB varieties. WD treatment also reduced fibre length and strength, with a more significant impact on LB varieties. In addition, WD significantly increased the relative protein content of cottonseed but decreased the relative oil content, leading to a decrease in seed vitality. Under WD irrigation, compared to seeds of LB varieties, the seeds of SB varieties have higher germination potential. Compared with LB varieties, SB varieties required less dry matter accumulation for boll maturation and produced more harvestable boll numbers, resulting in a smaller impact on yield and quality under WD irrigation. In general, SB varieties are more tolerant to WD stress and are expected to have a better performance in severe arid areas.