The present disclosure relates to the field of regulation of plant performance genes, in particular to a pectin methylesterase inhibitor gene GhPMEI39 and application of its encoded protein. The gene sequence of the pectin methylesterase inhibitor gene GhPMEI39 is shown in SEQ ID NO:1. According to the present disclosure, a public database is used to screen target genes, primers are designed to clone the target genes, its cotton transgenic materials and Arabidopsis thaliana transgenic materials are constructed, and plant development phenotypes after overexpression and constitutive expression of pectin methylesterase inhibitor protein are analyzed, and the role of the pectin methylesterase inhibitor gene GhPMEI39 in related functions such as plant flowering and inflorescence morphology is verified.
