Seafood is an important high-protein and low-fat food source prone to spoilage and may harbor food poisoning bacteria. Vibrio parahaemolyticus is a gram-negative halophilic bacterium that causes food poisoning. It is heat labile and can be eliminated through heating; however, V. parahaemolyticus may be present in seafood for raw consumption, such as sashimi. Recently, the use of bacteriophages or phages has been proposed as a non-thermal inactivation method for microbial control. Here, we characterized VF16, a novel phage that infects V. parahaemolyticus, and evaluated the effectiveness of the combination of VF16 with the antimicrobial amino acid d-serine in controlling V. parahaemolyticus through antimicrobial testing in broth cultures and raw scallops. The morphology of VF16 was examined using transmission electron microscopy, which demonstrated that it had a long, flexible tail characteristic of a siphovirus. Genome sequencing revealed that VF16 is a novel phage belonging to the family Demerecviridae, subfamily Ermolyevavirinae, and genus Vipunavirus. Analysis of adsorption and one-step growth curve in a liquid medium indicated that Ca2+ and Mg2+ are necessary for one or more subsequent replication processes of VF16 but are not essential for its adsorption. The combination of VF16 and d-serine completely inhibited the regrowth of V. parahaemolyticus in the liquid medium and effectively suppressed its growth in the scallop samples. No VF16-resistant mutants were isolated from the scallop samples treated with VF16 alone or in combination with d-serine. The combination of phages and d-amino acids is an effective non-thermal inactivation method for controlling foodborne pathogens.