Vibrio parahaemolyticus often contributes to a serious foodborne disease outbreak when marine mussels are consumed. The number of drug-resistant isolates of bacteria has also been increased, which makes clinical treatment more challenging. In general, a single food preservative cannot inhibit drug-resistant V. parahaemolyticus in seafood effectively. Inhibition effect of shrimp shell chitooligosaccharide (COS)-catechin (CAT) conjugate toward V. parahaemolyticus was studied. COS-CAT conjugate was able to inhibit V. parahaemolyticus with minimal inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 0.256 and 1.024 mg/L, respectively. Based on time-killing profiles, V. parahaemolyticus cells in shucked Asian green mussels were inactivated by 84% after 2 MIC (0.512 mg/mL) treatment for 6 h. The COS-CAT conjugate mainly caused membrane disruptions and damages as witnessed by numerous pores and concaves on the cell surface. Membrane damages were further confirmed by the increases in conductivity, extracellular malondialdehyde content, and potassium and magnesium ion leakages. Furthermore, the virulence factors of V. parahaemolyticus, involving extracellular polysaccharide, biofilm production and motility, were significantly inhibited. COS-CAT conjugate might attach to genomic DNA after cell deformation. Hence, COS-CAT conjugate could be used as a promising food-grade antibacterial agent, particularly against V. parahaemolyticus in the seafood sector.