As the most abundant biological entities on the planet, viruses are involved in global biogeochemical cycles, and they have been shown to play an important role in the overall functioning of the deep-sea ecosystem. Nevertheless, little is known about whether and how deep-sea viruses affect the physiology of their bacterial hosts. Previously, the filamentous phage SW1 was identified in the bathypelagic bacterium Shewanella piezotolerans WP3, which was isolated from the upper sediment of West Pacific ocean. In this study, phage SW1 was shown to be active under in situ environmental conditions (20 MPa and 4°C) by transmission electron microscopy and reverse-transcription quantitative polymerase chain reaction. Further comparative analysis showed that SW1 had a significant influence on the growth and transcriptome of its host. The transcription of genes responsible for basic cellular activities, including the transcriptional/translational apparatus, arginine synthesis, purine metabolism and the flagellar motor, were down-regulated by the phage. Our results present the first characterization of a phage–host interaction under high-pressure and low-temperature conditions, which indicated that the phage adjusted the energy utilization strategy of the host for improved survival in deep-sea environments.