GlpD is a key enzyme in glycerol metabolism that is commonly present in bacteria, and it regulates a diverse of bacterial activities. Vibrio splendidus is an important opportunistic pathogen in aquaculture, but the knowledge on its virulence is still limited. In this study, we investigated the role of glpD in V. splendidus by construction of a mutant strain AJ01/AglpD with an in frame deletion of the glpD gene. AJ01/AglpD mutant showed no difference in the growth when using 2216E medium, but it did not grow when using glycerol as the solo carbon source. AJ01/AglpD showed reduced virulence to clam Ruditapes philippinarum with attenuated swimming motility and haemolysis compared to that of the wild type AJ01. In order to further explore the genes and pathways regulated by GlpD, the cells of AJ01 and AJ01/AglpD were used for transcriptomic analysis. The results showed that there were 556 differentially expressed genes (DEGs), of which 276 genes were upregulated and 280 genes were downregulated in AJ01/AglpD. GO and KEGG analyses showed that the DEGs were mainly enriched in the citric acid cycle, oxidative phosphorylation, glycolysis, carbon metabolism, and ribosomes, which are frequently associated with material and energy metabolism in bacteria. Since the levels of the energy related metabolism were different in AJ01/AglpD, the persister cells in AJ01 and AJ01/AglpD were determined. The result showed that AJ01/AglpD exhibited decreased level of persister cells at both the exponential phase and the stationary phase. In summary, GlpD contributes to the pathogenicity and persistence of V. splendidus AJ01 by downregulating the citric acid cycle, oxidative phosphorylation, but upregulating glycolysis.