By using canonical correspondence analysis(CCA),this paper studied the relationship between phytoplankton species and its environmental factors. The speciesenvironment biplots were drawn based on the result of CCA. The result showed that total inorganic nitrogen, water temperature and transparency were the most important factors influencing the distribution of phytoplankton species. The distribution of main dominant phytoplankton species Chaetoceros muelleri and Eucompia zoodiacus correlated strongly with phosphate. CCA can be a useful tool to understand the spatial distribution of phytoplankton species in marine ecosystems.