Cytokinin oxidase/dehydrogenase (CKX) is a key regulatory enzyme for the irreversible degradation of the plant hormone cytokinin (CK), which is important in growth and development and response to abiotic stresses in cotton. In this study, 27, 28, 14 and 14 CKXs were screened by FAD structural domain and cytokinin binding structural domain in Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii, respectively. Their phylogenetic relationships and expression patterns were analyzed, and most GhCKXs were found to be tissue-specific and responsive to various abiotic stresses such as cold, heat, salt and PEG. GhCKX6b-Dt was selected for gene silencing in evolutionary branch II for salt stress, because its expression increased after salt stress in cotton plants. An increase in PRO and MDA content and a decrease in SOD activity due to this gene were found after inducing salt stress, contributing to oxidative damage and decreased salt tolerance. In this study, CKXs were analyzed to reveal the possible role of GhCKXs against abiotic stresses in cotton, which provides a basis for further understanding of the biological functions of CK in plants such as growth and development and stress resistance.