Abstract: Abstract: In the middle and lower reaches of Yangtze River, China, rain-waterlogging and high temperature occur simultaneously and have a high probability after rainfall in summer. Thus, they are the two limiting factors for cotton growth. It is unclear about the response of cotton to waterlogging under high temperature stress. This study investigated the growth and physiological metabolism characteristic of cotton seedlings under combination of waterlogging and heat stress. A pot experiment was conducted in Jingzhou, China during the growing season of cotton in 2013 using two-factor completely randomized block. Waterlogging and high temperature were designed as treatments. Waterlogging treatments included 0, 3, 6 and 9 days and the heat stress experienced continually for 0 and 3 days during the cotton seedling stage. Principal morphological indexes, chlorophyll fluorescence parameters and antioxidant enzymes of plants were measured at the end of experiment. The results showed that: 1) Morphological parameters of cotton crops were not significantly affected by high temperature stress when waterlogging duration was less than 3 days; but when waterlogging lasted for 3 days above, the constant high temperature condition could lower the plant height, leaf area and dry matter weight, and the roots to shoot ratio; the changes in these parameters induced by waterlogging under high temperature were generally 3 days earlier than that under the regular temperature; 2) The photosynthetic physiological indexes of the fourth leaves including chlorophyll (Chl) a, Chl b and photosystem II variable fluorescence to maximum fluorescence ratio, and fluorescence to original fluorescence ratio decreased with increasing waterlogging duration under the high temperature condition, but the ratio of Chl a and Chl b remained the same; 3) Under the natural temperature conditions, the antioxidant enzymes in roots and leaves including the superoxide dismutase (SOD) and peroxidase (POD) activity rapidly declined with the increment of waterlogging days, whereas malondialdehyde (MDA) was opposite; 4) Affected by the interactive effects of waterlogging and high temperature, the SOD and POD activities of leaves increased firstly and then decreased, their maximum and minimum values all occurred in the 3 and 9 days of waterlogging; the MDA content was increased obviously, indicating that the heat stress aggravated cell membrane damage degree; and 5) The waterlogging stress was the main limiting factor of cotton growth in the seedling stage, followed by heat stress; Moreover, there existed the significant interaction effects of Chl, Chl a, the ratio of Chl a and Chl b, and PS II maximum photochemical quantum yield as well as SOD, POD and MDA of leaves under the interactive influence of high temperature and waterlogging. The research may provide data support for cotton stress-resistance cultivation and drainage management in the middle and lower reaches of China.