In this study, the differentially expressed sequence ES816317 was cloned based on the differential expression sequence results of the low phosphorus stress gene expression profile chip in the roots of Gossypium hirsutum L. and the genome database. We used bioinformatics methods to analyze its nucleotide and protein. Its tissue expression pattern and relative expression under low phosphorus stress were detected by using qRT-PCR technology, so as to lay the foundation for analyzing the biological function of GhCSN6A in G. hirsutum and provide genetic resources for cotton phosphorus efficient genetic engineering breeding. The results showed that: (1) GhCSN6A gene of G. hirsutum L. was successfully cloned, and the full length of the open reading frame of the gene was 948 bp, encoding 315 amino acids. GhCSN6A protein, called COP9 signalosome complex subunit 6a, belonged to the MOV34 protein superfamily, had an MPN_CSN6 domain, and was localized in the nucleus. (2) Sequence alignment and evolution analysis showed that the similarity of GhCSN6A to HsCSN6A and AtCSN6A was 95.87% and 84.54%, respectively, so the gene was named GhCSN6A. (3) qRT-PCR analysis showed that GhCSN6A was expressed in all tested tissue including root, stem, leaf and flower, and the expression level was the highest in leaf, but there was no significant difference between leaf and root. The relative expression of GhCSN6A gene was the lowest in the root treated with low phosphorus for 24 h. However, the highest in the root treated with low phosphorus for 72 h, which was twice that of the suitable phosphorus (control) treatment. The study has speculated that GhCSN6A gene played an important role in the response to low phosphorus stress in G. hirsutum.