In this study, a soil culture experiment was set up in barrels to investigate the effect of waterlogging duration at different growth stages on the growth, yield, and quality of cotton in the Huang-Huai Region of China during summer. The experiment was conducted at four growth stages of cotton (seedling, squaring, flowering, and boll opening), and the waterlogging duration at each stage was set to five levels (2, 4, 6, 8, and 10 d) and the waterlogging depth was 5cm. Twenty different treatment combinations were established, and one group without waterlogging throughout the whole growth period was used as the control (CK). The results showed that the waterlogging treatments at the different growth stages reduced the morphological and yield parameters of the cotton plants as well as the physiological parameters of the cotton leaves, and the extent of the reduction in these parameters increased with the extension of the waterlogging duration. The effect of waterlogging at different growth stages on the cotton decreased in the order of the flowering, squaring, seedling, and boll-opening stages, and the highest yield reduction rates for the four stages were 38.8%, 27.9%, 18.3%, and 7.6% respectively. Additionally, waterlogging decreased the quality parameters of cotton such as the upper-half mean length, uniformity index, micronaire value, elongation, yellowness, and lint percentage at the squaring, flowering, and boll-opening stages. Furthermore, at the seedling stage waterlogging for no more than 6 d allowed the morphological and yield parameters to recover in the boll-opening stage upon timely drainage, and these parameters showed no significant decreases compared with the CK level. The critical duration of waterlogging at the squaring stage was 4 d. However, at the flowering stage, even 2 d of waterlogging could lead to the stagnation of morphological development and prevent the recovery of the cotton yield to the CK level. Therefore, when waterlogging disasters occur in cotton fields, the implementation of appropriate surface and subsurface drainage schemes for the different growth stages is needed as soon as possible to mitigate the damage.