A high-efficiency pyrethroid-degrading bacterium, Photobacterium ganghwense strain 6046 (PGS6046), was first isolated from an offshore seawater environment. Metabolomics method was used to investigate the biotransformation pathway of PGS6046 to cyfluthrin wherein 156 metabolites were identified. The growth rates of the PGS6046 cultivated in nourishing media were much higher than those cultivated in seawater, regardless of the presence of cyfluthrin. Statistical analyses revealed that the metabolic profile of PGS6046 was associated with the culture medium, the presence of cyfluthrin, and culture time. The PGS6046 cultivated in a nourishing medium was characterized by higher levels of amino acids, a lower abundance of intermediates in the tricarboxylic acid cycle, and the presence of some fatty acids than those cultivated in seawater. The effects of cyfluthrin on PGS6046 metabolism varied based on the culture medium, whereas the cyanoalanine levels increased under both culture conditions. Culture time significantly affected the metabolism of amino acids and carbohydrates in PGS6046. The present study revealed the metabolic characteristics of PGS6046 under different culture conditions and will further facilitate the exploration of the fundamental questions regarding PGS6046 and its potential applications in environmental bioremediation.