Identifying important regulative elements and pathways related to dwarfism in cotton is a major challenge in cotton breeding. Isobaric tags for relative and absolute quantitation-based proteomics of stem terminal buds from upland cotton (Gossypium hirsutum L.) dwarf line LA-1 and high near-isogenic line LH-1 was performed. Moreover, transcriptional expression of differentially-expressed proteins (DEPs) belonging to phytohormone signal transduction, hormone biosynthesis, and ubiquitin system were analysed using quantitative real-time polymerase chain reaction. A total of 4 849 proteins were identified from LA-1 and LH-1, 697 of which showed differential accumulations. Most of the DEPs have catalytic, binding, and transporter activity and are involved in metabolism- and protein processing-related pathways. In particular, seven DEPs, including two gibberellin (GA) receptors, three cytokinin (CK) receptors, CKoxidase, and CK-N-glucosyltransferase were up-regulated in LA-1, and GA20-oxidase was down-regulated in LH-1. Our results suggest that the DELLA-independent GAsignalling pathway is the primary cause of dwarfism in LA-1 and indicate that CKresponse element 1-2, GA-insensitive dwarf, CKoxidase, and GA3-β-dioxygenase are potential indicators of dwarf cotton. The profiling of DEPs may offer a valuable resource for cotton breeding.