Abstract: To test the effects of different external nutrient loading on characteristics of phytoplankton community structure, a whole-ecosystem nutrient addition experiment was conducted in 4 ponds located at the Yangtze River Basin from December 2010 to June 2012. Four treatments were set to represent various nutrient loads, namely both nitrogen (N) and phosphorus (P) addition (+N+P), P addition (−N+P), N addition (+N−P), and no nutrient addition (−N−P) (Control). In terms of species number, all treatments showed similar characteristic with the species number of 75, 79, 75 and 75 in −N+P, +N+P, +N−P and Control respectively, and Chlorophyta were the dominant taxonomic group followed by Cyanophyta. In terms of functional group, the percentage of meso-eutrophic species in −N+P was similar to that in +N+P, both were higher than the two treatments without adding P. The percentage of oligotrophic species in +N−P was higher than that in +N+P treatment, and even higher than the Control. The above results suggest that the reduction of nitrogen cannot control the percentage of moso-eutrophic species of phytoplankton, while the reduction of P can induce the succession of phytoplankton community from a meso-eutrophic type to an oligotrophic type. These results provide theoretical foundation for N management strategy in mitigating eutrophication to a certain extent.