The deep sea is one of the least-explored ecosystems on Earth. Deep-sea virus communities are crucial components of this ecosystem and play crucial roles in food webs and biogeochemical cycles. Viruses that infect bacteria and archaea in the deep sea regulate microbial abundance and community structure, thereby influencing nutrient cycling throughout the deep sea and extending to the global ocean. By manipulating microbial communities through cell lysis, viruses promote the release of organic carbon and enhance the host’s ability to adapt to extreme environments through the expression of auxiliary metabolic genes during host infection. This adaptation enables virus to thrive in the deep sea via lysogenic life strategies. However, our knowledge of deep-sea viruses remains limited. This review explores the importance of viruses in deep-sea ecosystems, focusing on their community structure, diversity, interactions with host cells, ecological functions, and impacts on biogeochemical cycles. It also highlights current challenges in deep-sea virology and provides prospects for future research into deep-sea viruses.