Upland cotton (Gossypium hirsutum L.) is one of the world’s most important fiber crops, accounting for more than 90% of all cotton production. While their wild progenitors have relatively short and coarse, often tan-colored fibers, modern cotton cultivars possess longer, finer, stronger, and whiter fiber. In this study, the wild and cultivated cottons (YU-3 and TM-1) selected show significant differences on fibers at 10 day post-anthesis (DPA), 20 DPA and mature stages at the physiological level. In order to explore the effects of domestication, reveal molecular mechanisms underlying these phenotypic differences and better inform our efforts to further enhance cotton fiber quality, an iTRAQ-facilitated proteomic methods were performed on developing fibers. There were 6990 proteins identified, among them 336 were defined as differentially expressed proteins (DEPs) between fibers of wild versus domesticated cotton. The down- or up-regulated proteins in wild cotton were involved in Phenylpropanoid biosynthesis, Zeatin biosynthesis, Fatty acid elongation and other processes. Association analysis between transcroptome and proteome showed positive correlations between transcripts and proteins at both 10 DPA and 20 DPA. The difference of proteomics had been verified at the mRNA level by qPCR, also at physiological and biochemical level by POD activity determination and ZA content estimation. This work corroborate the major pathways involved in cotton fiber development and demonstrate that POD activity and zeatin content have a great potential related to fiber elongation and thickening.