The invention provides a cotton GbGUT1 gene, an encoding protein thereof and application. Open reading frame sequences of a gene are 1239bp and are shown as SEQ ID NO.1; an expression vector of the cotton GbGUT1 gene contains the gene; the expression vector can be applied to improving crop varieties and cotton fiber quality. The cotton GbGUT1 gene, the encoding protein and the application have the advantages that the cotton GbGUT1 gene which is a glucuronic acid transferase gene is an important enzyme in pectin metabolic pathways and has important relations with cotton fiber development, accordingly, novel candidate genes can be provided for cotton fiber quality improvement genetic engineering, foundation can be laid for further converting cotton to improve the cotton fiber quality, and the cotton GbGUT1 gene and the encoding protein have high application value.