Lake Taihu, a shallow lake located in the eastern plain of China, has been plagued by eutrophication and cyanobacterial outbreaks due to the highest population density and industrial and agricultural development in the region. Total phosphorus concentrations have fluctuated at high levels while total nitrogen concentrations have continued to decrease in Lake Taihu since 2016. The release of endogenous phosphorus from algal cells is an important source of total phosphorus in the lake, and the level of polyphosphate (PolyP), a reservoir of phosphorus in algal cells, significantly affects the release of endogenous phosphorus from algal cells. In response to this phenomenon, we conducted a study on the potential of phosphorus utilization, especially polyphosphate synthesis by blooming cyanobacteria and Microcystis aeruginosa under different nitrate nitrogen concentrations. By measuring the photosynthetic activity and antioxidant system activity of M. aeruginosa under low nitrate nitrogen concentration, we explored the physiological mechanism that how low nitrate nitrogen concentration promotes the excessively synthesis of PolyP in Microcystis. The results showed that both blooming cyanobacteria and M. aeruginosa had luxury uptake of PO₄^3- and intracellular accumulation of PolyP if the nitrate nitrogen concentration was below 2 mg/L, while the intracellular protein dry weight (0.6 mg/mg) of M. aeruginosa also decreased significantly due to the decrease of available nitrogen elements in water. Meanwhile, the photosynthetic activity of M. aeruginosa could still reach 75.1%-88.7% of the control group, but due to the decrease of carbon and nitrogen assimilation capacity, the relatively strong photosynthetic activity led to the accumulation of intracellular reactive oxygen species, which put the cells in an oxidative stress status to induce the activation of antioxidant system. The dual dilemma of low nitrogen content and oxidative stress prompted cyanobacterial cells to synthesize PolyP in large quantities to prevent the damages of protein, nucleic acid and cell membrane structure in cyanobacterial cells. Thus, the adverse conditions of nitrogen deficiency led to increase cyanobacterial intracellular phosphorus content. If the cyanobacterial cells decayed, a large amount of PO₄^3- was released into the water column to cause the increase of total phosphorus in water body under the low nitrate nitrogen condition.