Abstract: To investigate the potential influence of nitrogen and phosphate on phytoplankton community structure, we conducted field experiments and enrichment incubation experiments in Nansha area the southwest continental shelf and near the James shoal area: S1 (9°30′N, 109°30′E) and S2 (4°30′N, 109°30′E) in summer of 2013. The results show that: 1) The number of phytoplankton species increased after enrichment; 2) Shannon-Wiener diversity index declined with increasing nutrient concentration; 3) Pyrrophyta and Bacillariophyta were the dominant species before and after the enrichment incubation, respectively. Pyrrophyta had more competitive advantages than Bacillariophyta in the oligotrophic region, leading to the shift from Pyrrophyta to Bacillariophyta; 4) Nutrient enrichment caused rapid growth of phytoplankton in a short time, but it inhibited phytoplankton growth when exceeding a certain level and the inhibition was associated with the phytoplankton species; 5) With increasing nutrients concentration in each group, the abundance of Pyrrophyta and Bacillariophyta in single N and single P groups had little change, but the abundance of Pyrrophyta in mixed N and P groups decreased significantly, and the abundance of Bacillariophyta increased significantly. Mixed N and P limited the phytoplankton growth.