Pseudomonas plecoglossicida is a pathogen that causes visceral white spot disease that results in significant financial losses. Valine-glycine repeat protein G (VgrG) is one of the core components that make up the spike structure in the type VI secretion system (T6SS), which transports effectors and then contributes to bacterial virulence. However, the specific effect of VgrG on bacterial infection and host response process has not been clearly explained. Herein, we compared the pathogenicity of vgrG gene-deleted (ΔvgrG) strain, vgrG gene-complemented (C-ΔvgrG) strain, and the wild-type (NZBD9) strain of P. plecoglossicida to hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂). Compared to the wild strain, lost vgrG led to a higher survival rate, a lower bacterial load, and several mild pathological changes, such as fewer white nodules on the surface of the spleen and attenuated tissue damage. Moreover, the RNA-Seq of grouper spleen post-challenge indicated 3205 DEGs were involved in the two antibacterial responses, and the antigen presentation and processing pathway and the T-cell receptor signaling pathway were principal significant enrichment items. In summary, our data suggested that deletion of vgrG gene might reduce the pathogenicity of Pseudomonas plecoglossicida on hybrid grouper by making it less able to colonize the host and more easily cleared by the host immune system.