Phytoplankton samples from typical stations along the East China Sea and the northern south China sea were analyzed by RP-HPLC combined with DAD (diode array detector) to determine pigments composition. Ocean study included PN section along East China sea(September in 2002) and northern of south China sea(November in 2002). Pigments data were transformed into phytoplankton composition by software CHEMTAX based on least square method and steepest descent algorithm. This work showed that phytoplankton communities in PN transect were clustered into two types, mostly influenced by stratification. Communites in upper layer were dominated by cyanobacteria, while diatoms were most important groups in lower layer. Also two types of phytoplankton community structure in S transect were clustered by the distance from the shore. Diatoms, Cryptophyta, Chlorophyta were main groups in shore, and Prymnesiophyta, Cyanobacteria, Prochlorophyta were main groups offshore. Additionally,primary analysis was carried out to illuminate the relationship of phytoplankton community structure and environmental factors.