[Objective] This study aimed to determine activities of antioxidant enzymes during gland morphogenesis in cotton, thoroughly explore physiological changes of cotton and provide a scientific basis for the cultivation of excellent cotton varieties. [Method] Based on determination of gossypol contents and antioxidant enzymes ac- tivities during gland morphogenesis in three cotton varieties (Chuanmian2802, Xiang- mian18 and XianwuN5), metabolism of gossypol and morphogenesis of gland in cot- ton were explored. [Result] After gland morphogenesis, the content of gossypol in Chuanmian2802 was gradually reduced in the early period of seed germination, which slowly increased since the 5th d after germination; however, during the seed germination period, the content of gossypol in Xiangmian18 had a slowly increasing trend and was gradually close to the content of gossypol in Chuanmian2802. The results showed that activities of SOD, POD and CAT increased in seed germination, which was contributive to remove the superoxide radicals, decrease the peroxide lev- el, reduce damages to the membrane, enhance the body's resistance to lipid oxida- tion and increase resistance ability to stress. [Conclusion] This study laid the scientif- ic foundation for understanding the characteristics of gland morphogenesis in cotton and cotton cultivation by using gland traits.