The level of nutrients in sea waters, such as N, P, etc., are believed to have impacts on plankton structures (total species number, species richness, species evenness, the diversity index, and diversity threshold value). In order to explore the biological and ecological impacts of N and P in the coral reef near Weizhou Island, N∶P ratio in different N and P forms and their relationship with plankton structures were analyzed based on the data collected from December 2007 to October 2008 in the coral reef near Weizhou Island. The result showed that ratio of N∶P in the coral reef near Weizhou Island was high and its annual-mean value was 38.08±14.7, suggesting that the sea area was obviously constrained by P. In general, seasonal variation of N∶P is influenced by wind-driven currents and consequently N∶P is much higher in winter and summer than in spring and autumn. Spatial variation of N∶P was influenced by some factors related to locations. In the sea areas of northeast and northwest where coral cover and primary biomass were higher, ratios of dissolved organic nitrogen (DON) over dissolved organic phosphorus (DOP), dissolved nitrogen (DN) over dissolved phosphorus (DP), and total nitrogen (TN) over total phosphorus (TP) were all higher. In the sea areas of north and southwest where wind-driven currents’ influence was stronger, ratios of dissolved inorganic nitrogen (DIN) over dissolved inorganic phosphorus (DIP) and particulate nitrogen (PN) over particulate phosphorus (PP) were much lower. In the sea area of south where pollutions of domestic sewage and sea farming were obvious, PN∶PP was the highest. The temporal and spatial variation of N∶P reflected the influence of ecosystem, wind-driven currents and human activities on the release, transfer, and supply of nutrients. Correlation analysis revealed the ratios of N∶P in different N and P forms were correlated one another significantly in spring and summer when southwest monsoon prevailed, somewhat significantly in winter when northeast monsoon prevailed, and not significantly in autumn. The ratios of N∶P in different N and P forms were influenced more obviously by environmental factors in autumn and winter when northeast monsoon prevailed and in spring when cold water mass appeared. The influence of N∶P on the structure of plankton was much greater than the environmental factors. In autumn when zooplankton and phytoplankton flourished, DON∶DOP and DN∶DP were positively correlated with the total species number, species richness, species evenness, the diversity index, and diversity threshold value of zooplanktons; in spring when zooplankton and phytoplankton were comparatively less, DIN∶DIP and PN∶PP were negatively correlated with the species richness and diversity index of phytoplankton (P≤0.05), and DON∶DOP, DN∶DP, and TN∶TP were positively correlated with species evenness of phytoplankton and negatively correlated with the diversity threshold of phytoplankton, indicating that in the coral reef it was the ecological process that plays a leading role in influencing the N∶P ratio. Among the N∶P ratios in five N and P forms, DON∶DOP ratio’s influence on primary biomass and biological structure of coral reef ecosystem was the greatest.