Multidrug-resistant Vibrio parahaemolyticus has become a significant threat to human health and prioritizing the development of effective drug and vaccine candidates. Hence, a total of 4822 proteins were screened from V. parahaemolyticus proteome to find out effective drug and vaccine targets using a comprehensive genome-based analysis. Among 16 novel cytoplasmic proteins, 'VIBPA Type II secretion system protein L' and 'VIBPA Putative fimbrial protein Z' were allowed to molecular docking with 350 human metabolites, which revealed that Eliglustat, Simvastatin and Hydroxocobalamin were the top drug molecules. Experimentally, three subunit vaccines were constructed by the combination of highly antigenic epitopes along with suitable adjuvant, PADRE sequence and linkers. The designed vaccine constructs (V1, V2, V3) were analyzed and molecular docking with MHC molecules that suggested the superiority of construct V1. Besides, the binding affinity of human TLR1/2 heterodimer and construct V1 could be biologically significant in the development of the vaccine repertoire.