Annually occurred cyanobacterial bloom aggravated eutrophication situation and changed the lacustrine ecosystem components. Recently, high concentration of bloom cyanobacteria had been found to accelerate total nitrogen (TN) removal. However, the contribution of cyanobacterial bloom to TN removal remained unclear. In this study, microcosms with different density of bloom cyanobacteria were constructed and quantitative PCR and structural equation modelling (SEM) were used to analyze the microbes, environmental variables and the causal relationship to TN removal. Total bacteria, ammonia-oxidizing archaea and nirS gene abundances were indirectly influenced by cyanobacteria biomass and all of them had a direct effect on TN removal. SEM confirmed that cyanobacteria made a direct contribution to ammonium‑nitrogen (NH-N) level in water and induced nitrification activity, which favored the process of denitrification by supplying substrate and aggravating the anoxic status. These results strongly suggested that an increased cyanobacteria biomass had strong impacts on mineralization, nitrification and denitrification by mediating TN, dissolved organic carbon and dissolved oxygen directly and subsequently influenced the nitrifiers and denitrifiers.