Abstract: Drought is a serious, worldwide problem for crop production and also affects yields of cotton. This paper conducted on different drought resistance of 41 cotton germplasm at germination stage by the experiment of 15%PEG6000 vertically rolled paper tests.We determined 8 indentification indices such as germination energy, germination rate, seedling length of 3 days, total seedling fresh biomass of 3 days, hypocotyl length of 7 days, radicle length of 7 days, radicle length of 7 days/Hypocotyl length of 7 days, growth rate of sprout length. The results showed that the 8 indices were lower under 15%PEG6000 than water controlled condition and the coefficients of variation became bigger except for total seedling fresh biomass of 3 days indicating that cotton germination was inhibited by 15%PEG6000 and the different varieties(lines) were evidently different. At the same time the relative values of T/CK were calculated. We screened 7 indentification indices such as relative germination energy, relative germination rate, relative seedling length of 3 days, relative hypocotyl length of 7 days, relative radicle length of 7 days, relative radicle length of 7 days/Hypocotyl length of 7 days, relative growth rate of seedling length by the way of variance analysis and principal component analysis. The results showed that this 7 indices had some connection with germination drought resistance. The subordinate function values of cotton germplasm under PEG6000 drought treatment and the correlation coefficient were analyzed by the 7 indices. The average subordinate function values stood for ability of germination drought resistance. With the increase of the average subordinate function values the cotton germination drought resistance ability was increasing. The results showed that relative radicle length of 7 days was significantly related to the average subordinate function values(r=0.839**). There were 7 accessions of cotton germplasm with high drought resistance ability at germination stage such as Ji668,Lumianyan21, 9409xuanxi,DP99B,Chuangmina22, sGKZhong980,Han177 and 10 accessions of cotton germplasm with medium drought resistance ability such as Zhong23A-12,Zhong23AkanmianF12,CRI35,Ji1286, GKZ19F6,Shuangyu97-2067,Guangzi2,Naigaowen-2,ZhongS9612, Guangzi1.