Diel rhythms structure microbial activity in the ocean, yet the role of viral lysis in driving short-term community dynamics remains poorly understood. Here, we combined dilution experiments, high-resolution microbiome sampling and extracellular ribosome sequencing to investigate diel virus-host interactions in the South China Sea. Viral lysis accounted for average of 41% of Synechococcus and 24% of heterotrophic bacterial mortality at night. Overall, 74% of amplicon sequence variants (ASVs) showed lysis signals, with many displaying significant diel fluctuations. Notably, rare taxa comprised a large fraction of diel-responsive ASVs, indicating high turnover among low-abundance populations. Synechococcales exhibited tightly coupled nighttime peaks in abundance and lysis, while SAR11 and Flavobacteriales showed delayed lysis after late-day growth. In addition, virus-mediated mortality had a stronger influence on metabolically active and diel-responsive ASVs. These findings highlight viral lysis as a temporally structured and taxon-specific force sustaining microbial turnover and diversity in oligotrophic waters.