Eutrophication caused by human activities has severely impacted freshwater ecosystems, leading to harmful cyanobacterial blooms that threaten water quality and ecosystem stability. During blooms, denitrification is a key process for nitrogen removal, which can occur both in the sediment and in the waterbody mediated by cyanobacterial aggregate (CA)-associated microorganisms. In this study, the structure, dynamics and assembly mechanisms of CA-associated nirK-, nirS-, and nosZ-encoding denitrifying communities were investigated in the eutrophic Lake Taihu across the bloom season. External environmental factors showed limited influence on denitrifying community structure, which were more strongly shaped by biotical factors. Network analysis revealed both monofunctional and multifunctional modules, with a small subset of linker OTUs playing a critical role in maintaining these multifunctional modules by mediating interactions among different functional communities. Biotic regulation was further demonstrated by coupling patterns among denitrifiers associated with specific microbial lineages, as well as niche partitioning driven by cyanobacterial composition. While the assembly of the total phycospheric communities was governed by stochastic processes, the denitrifying communities were predominantly shaped by homogeneous selection. These findings indicate biological processes, particularly synergistic relationships and autotroph-heterotroph interactions, were key drivers of the structure and dynamics of denitrifying communities within CAs. Moreover, the key taxa identified in this study may provide potential targets for regulating nitrogen cycling in the management of cyanobacterial blooms.