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In order to reveal the response of cotton to waterlogging stress, lysimeter experiments were conducted in the Irrigation and Drainage Experiments Station of Wuhan University during 2008—2011. Effects of different waterlogging forms (surface waterlogging, subsurface waterlogging and the combination of both) and different occurring growth stages (bud stage, flowering and boll setting stage or boll opening stage) on cotton morphology (leaf area index (LAI), stem diameter and plant height) and yield (seed cotton and dry matter) were discussed. Structural equation modelings (SEM) of yield and morphology characteristics related to waterlogging stress were established. Interactive relationships between these models were analyzed. The results showed that subsurface waterlogging stress inhibited the development of cotton morphology less than that of surface waterlogging stress, while the combination of surface and subsurface waterlogging stresses inhibited the growth most. Waterlogging stress occurred in bud stage, flowering and boll setting stage inhibited the development of morphology characteristics significantly (p<0.05), while the inhibiting effect at boll opening stage was not significant. LAI, followed by stem diameter and plant height, was the most sensitive morphology index to describe the response of cotton morphology to waterlogging stress. The cotton yield reduction with subsurface waterlogging stress was less than that with surface waterlogging stress, while the reduction was almost the same when surface waterlogging stress or subsurface-surface waterlogging stress was occurred. Waterlogging stress occurred at flowering and boll setting stage reduced the yield most, followed by bud stage and boll opening stage in sequence. And the inhibiting effects of waterlogging stress on seed cotton yield were more than that on dry matter yield. According to SEM analysis, waterlogging stress effects on yield were more than that on morphology characteristics, and waterlogging temporal indices (SWFDH and SEW30) were better than spatial indices (SFW and SEW30) and SFEW30 in describing waterlogging stress effects on growth and yield of cotton.