The two-component systems (TCSs) play vital roles in the regulation of a series of biological processes in bacteria, and the CpxA-CpxR is considered as a kind of classical TCSs involved in bacterial envelope stress responses. However, the roles of the CpxA-CpxR are not sufficiently understood in Vibrio alginolyticus, a serious pathogen causing the outbreak of pathogenic diseases vibriosis in marine fishes. In this study, we examined the effect of cpxA and cpxR deletion on typical phenotypes of V. alginolyticus HY9901, and the result showed that deletion of cpxA and cpxR and increased the susceptibility to high salinity, iron limitation, certain antibiotics (kanamycin and midecamycin), but had no effects on growth curve and swarming motility of V. alginolyticus. Besides, deletion of cpxA (not cpxR) decreased biofilm formation of V. alginolyticus. In addition, the stimulation of ΔcpxA and ΔcpxR significantly up-regulated the expression of immune-related genes in grouper spleen (GS) cells compared to WT, and deletion of cpxA and cpxR decreased the bacterial adhesion and intracellular ferrous iron concentration in GS cells, and increased the viability of infected-GS cells. Consistently, deletion of cpxA and cpxR decreased bacterial invasion and intracellular replication in grouper primary macrophages. The present study thus improves the understanding of the functions of the CpxA-CpxR system in gamma proteobacteria, and also provides new insight into the molecular pathogenesis of vibriosis in marine fishes.