Vibrio parahaemolyticus is a major seafood-associated foodborne pathogen whose lipopolysaccharide (LPS) plays an important role in virulence and antimicrobial resistance. The LPS of V. parahaemolyticus contains a single 3-deoxy-D-manno-octulosonic acid (Kdo) sugar with phosphorylation. Previously, we have characterized the gene VP_RS01035 is responsible for the addition of Kdo; in this study, we characterized another gene VP_RS00960 which is responsible for the Kdo phosphorylation of V. parahaemolyticus LPS. To investigate its function, we first constructed an LPS-deficient Escherichia coli WH600 strain using CRISPR/Cas9. Heterologous expression of VP_RS01035 alone or in combination with VP_RS00960 yielded recombinant strains WH600/pB1-1 and WH600/pB2-12, respectively. Analysis of total lipids from the recombinant strains by thin-layer chromatography and high-performance liquid chromatography-tandem mass spectrometry demonstrated that the VP_RS00960 gene encodes a Kdo kinase responsible for phosphorylating the 4-OH site of the Kdo sugar in V. parahaemolyticus. To further validate its role, we deleted VP_RS00960 gene in V. parahaemolyticus, resulting in mutant ΔRS00960. Notably, ΔRS00960 failed to produce polysaccharide-linked lipid A, although free lipid A synthesis remained unaffected. Furthermore, defective long-chain LPS assembly compromised outer membrane integrity, increasing permeability and hydrophobicity while reducing biofilm formation. Consequently, ΔRS00960 exhibited heightened susceptibility to membrane-targeting antibiotics, such as erythromycin and novobiocin. Macrophage infection assays using RAW264.7 cells revealed that VP_RS00960 deletion attenuated bacterial pathogenicity. These findings enhance the understanding of the pathogenicity and drug resistance of V. parahaemolyticus, and provide novel insights and strategies for addressing antibiotic resistance and food safety challenges posed by V. parahaemolyticus.