Microcystis aeruginosa, dominance specie in the cyanobacterial bloom, was cultured under the different initial pH values in order to study the effect of the growth of M. aeruginosa on the pH value and the nitrogen transformation in the medium. The results showed that the pH value rose in the lag phase and exponential phase of M. aeruginosa, and the maximum pH values rose from 7.2, 8.0 and 8.8 to 10.02, 10.34 and 10.94 respectively, then decreased in the stationary phase and the decline phase of M. aeruginosa. While initial pH value was 8.8, it decreased to 8.66 at the end of the experiment. NO3-concentration decreased and NO2-concentration rose earlier then decreased later in the medium during the growth period of M. aeruginosa. Both the concentrations of NO3-and NO2-decreased next to zero in the 60th and the 67th days, respectively. Compared with the initial total nitrogen content, the final total nitrogen contents decreased 25.97%, 27.52% and 28.16% under different initial pH values, respectively. The nitrogenous compound was transformed to N2 through denitrification. Thus, there is distinct decrease of nitrogenous compound by denitrification in M. aeruginosa bloom.