Harmful cyanobacterial blooms pose severe threats to aquatic ecosystems. Bloom-forming cyanobacteria form cyanobacterial aggregates (CAs) that create a phycosphere supporting diverse microbial interactions. Here, longitudinal metagenomics and metatranscriptomics were employed to explore the temporal variation of CA-attached viral communities throughout cyanobacterial blooms in Lake Taihu. Viral communities, represented by 5613 viral operational taxonomic units, showed increased relative abundance (RPKM) with the expansion of bloom areas. Among 1791 virus‒host linkages, host shifts followed the succession of two dominant cyanobacterial genera, Microcystis and Dolichospermum. Viruses demonstrated high virus‒host abundance ratios within all host genera and showed elevated transcriptional activities infecting Dolichospermum during the late bloom stage. Viruses featured high microdiversity and positively selected replication-associated genes in response to abundant host genera and variable trophic status. This study uncovered diverse active viral auxiliary metabolism associated with photosynthesis, biochemical cycling, and DNA biosynthesis, and highlighted the significant role of phycosphere-associated viruses during cyanobacterial blooms.