β-1,4-glucanase can not only promote the wound healing of grafted seedlings but can also have a positive effect on a plant’s cell wall construction. As a critical gene of β-1,4-glucanase,GH9Bis involved in cell wall remodeling and intercellular adhesion and plays a vital role in grafting healing. However, theGH9Bfamily members have not yet been characterized for melons. In this study, 18CmGH9Bswere identified from the melon genome, and theseCmGH9Bswere located on 15 chromosomes. Our phylogenetic analysis of theseCmGH9Bgenes andGH9Bgenes from other species divided them into three clusters. The gene structure and conserved functional domains ofCmGH9Bsin different populations differed significantly. However,CmGH9Bsresponded to cis elements such as low temperature, exogenous hormones, drought, and injury induction. The expression profiles ofCmGH9Bswere different. During the graft healing process of the melon scion grafted onto the squash rootstock, both exogenous naphthyl acetic acid (NAA) and far-red light treatment significantly induced the upregulated expression ofCmGH9B14related to the graft healing process. The results provided a technical possibility for managing the graft healing of melon grafted onto squash by regulatingCmGH9B14expression.