Viruses have an important ecological impact on the biological evolution, biogeochemical cycle, and coral diseases in coral reef ecosystems. With the global degradation of coral reefs, the functions and hazards of viruses in coral reef regions have become increasingly prominent. In this article, recent researches on viruses in coral reef ecosystems were reviewed, which included:(1) The diversity and distribution characteristics of viruses in coral reef ecosystem (sea water, host and core coral virome); (2) Ecological function of viruses in coral reef ecosystem (infection pattern, promoting biological evolution, and biogeochemical cycle); (3) Viruses response to global climate change in coral reef ecosystem (thermal stress and coral diseases). Accordingly, coral reef ecosystems have an extremely high viral richness and diversity. About 60 virus families are reported in coral reef ecosystems around the world, which account for 58% of all known viral families. Also, the core coral virome is manly composed of double-stranded DNA virus (dsDNA virus), single-stranded DNA virus (ssDNA virus) and retrovirus. The viruses in coral surface mucus layer are more abundant and diverse, due to enrichment with viruses from around environment in coral reef ecosystem. "Piggyback-the-Winner" is the main biodynamic mode of viruses in coral reefs, which indicates that viruses can promote the evolution of organisms by horizontal gene transduction in reef regions. In addition, viruses can participate in the carbon and nitrogen cycles of coral reefs by lysing bacteria and planktonic algae, respectively, which plays an important role in biogeochemical cycles of coral reef ecosystem. It's worth noting that viruses have ability to mediate coral thermal bleaching, which has closely associations with Phycodnaviridae and Herpesviridae. Moreover, viruses can also lead to coral diseases (e.g., white plague, white band disease and yellow blotch), which can affect the adaptability and resilience of coral reefs to global climate change. Herein, based on a systematic review of international research progress and current ecological status of coral reefs in the South China Sea, this article proposes the following research directions, in order to promote the development of coral reef virology:(1) The diversity and spatial-temporal distribution characteristics of viruses in coral reefs from the South China Sea; (2) The mediation effect of viruses on coral thermal bleaching and diseases in the South China Sea, and their relationship with intensified global climate change; (3) The contribution of viruses in biogeochemical cycles (e.g., carbon and nitrogen cycles) of coral reef ecosystems in the South China Sea.