Abstract: The aim is to provide a theoretical basis for waterlogging-resistance breeding and waterlogging - evaluating indicator screening of cotton. 9 cotton varieties (lines) were used as materials with split plot experiment. In cotton bud stage, the effects of different waterlogging days (10 days and 20 days) on the physiological indicator, yield and quality indicators were analyzed. And then screen the waterloggingresistance varieties (lines) and waterlogging- sensitive varieties (lines). The results showed that: (1) MDA contents, dry weight per plant, boll weight, and fiber quality could be used as evaluating indicators of waterlogging resistance; (2) when the waterlogging stress lasted for 10 days, MDA contents of different cotton varieties (lines) were significant higher than that of the control(P<0.01),‘Shan6353’had the highest sum of embership function value, followed by‘Ganza108’and‘Nantong87-1220’, and the value was 2.76, 2.23 and 1.68, respectively, while‘ZhongCJ-1’and‘Jinza88F1’had relatively low value; (3) when the waterlogging stress lasted for 10 days, dry weight per plant significantly decreased compared with that of the control (P<0.01), the sum of membership function values of‘Ganza108’,‘C111’,‘Nantong87-1220’and‘Shan6353’ were relatively high, which was 2.11, 2.13, 2.55 and 2.19, respectively; while‘Xumian21’and‘Han8942’ had relatively low sum of membership function values; (4) when waterlogging stress lasted for 10 days, boll weight was significantly lower than that of the control (P<0.01), ‘Ganza108’,‘Nantong87- 1220’and ‘Shan6353’had little reduction degree, compared with the control; and their sum of membership function values were 1.00, 0.96 and 0.80, respectively; while‘JS11’(0.00),‘Jinza88F1’(0.04),‘ZhongCJ-1’(0.26), ‘Xumian21’(0.30) and‘Han8942’(0.33) had relatively low valuest; (5) the sum of membership function values of upper half mean length, fiber strength and elongation appeared in‘Ganza108’,‘Shan6353’and ‘Nantong87-1220’with higher values of 2.46, 2.17 and 1.75, respectively; while‘JS11’(0.53) and‘Han 8942’ (1.03) had relatively low values. In conclusion,‘Ganza108’and‘Shan6353’were waterlogging-resistance varieties, while‘Han8942’and‘Jinza88F1’were waterlogging-sensitive varieties.