The formation and accumulation of massive Microcystis colonies was important to outbreak of Microcystis blooms. The concentration of nitrogen and phosphorus was one of the important factors affecting growth of Microcystis colony. This study was conducted to reveal the effect of different concentrations of nitrogen and phosphorus on the growth of Microcystis flos-aquae colonies. We took the mean ratio of nitrogen to phosphorus in Meiliang Bay in Lake Taihu as a reference, where was a serious region of Microcystis bloom in the past several years. The concentrations of nitrogen and phosphorus were set up to five treatments:T1:TN=0.1 mg/L, TP=0.005 mg/L; T2:TN=1 mg/L, TP=0.05 mg/L; T3:TN=10 mg/L, TP=0.5 mg/L; T4:TN=100 mg/L, TP=5 mg/L; T5:TN=250 mg/L, TP=5.44 mg/L (the concentration of BG-11 medium). The results showed that the size of M. flos-aquae colonies increased and the sizes of colony above 100 cells were 151, 217, 437 and 160 cells in treatments of T1, T2, T3 and T4, respectively. However, the size of M. flos-aquae colonies increased in initial stage of the experiment and then decreased in later stage of the experiment, and no colony of 100 + cells was found in treatment T5 during the whole experiment. The results indicated that relatively low concentration of nitrogen and phosphorus was beneficial for the growth of Microcystis colony, while high concentration might inhibit growth of Microcystis colony. This study also suggested that current concentration of nitrogen and phosphorus in Lake Taihu was in favor of the growth of Microcystis colonies which was conducive to the formation of Microcystis blooms.