In order to clarify the response of phytoplankton community structure to the meso-scale eddies in the South China Sea(SCS),three cruises were carried out,including aiming at a cyclonic eddy(CE)in the western SCS in early September 2007;three long lived anticyclonic eddies(ACEs)in the basin from 28 July to 7 August 2007;and a Rossby eddy in the northern SCS in January 2010,respectively.The photosynthetic pigments were detected by high-performance liquid chromatography(HPLC)to calculate the contribution of nine phytoplankton groups to TChl a biomass through CHEMical TAXonomy.Our results showed that the deep chlorophyll a maximum layer(DCML)was raised to form a dome structure in the CEs center while there was no distinct enhancement for TChl a biomass.However the TChl a biomass in the surface layer(at 5 m)in the eddy center was promoted 2.6-fold compared to the biomass outside the eddy(P<0.001).The phytoplankton community was primarily contributed by diatoms,prasinophytes,and Synechococcus at the DCML within the eddy,while less was contributed by haptophytes_8 and Prochlorococcus.We assumed that there was a gently continuous nutrient supply resulting from the doming of the isopycnal within the eddy while the increasing of phytoplankton TChl a biomass was remarkable at the surface layer even though the hydrological and nutrient signals were weak.The TChl a inventory was almost similar among the three ACEs(17.647~18.868 mg m-2),so did the predominant phytoplankton groups,haptophytes_8 and Prochlorococcus.The TChl a inventory was 20.822±3.026 mg m-2 at the edge which was 33%and 60%higher than those at the center and reference,respectively.The most prominent enhancement of biomass at the edge was provided by haptophytes_8,with 1.6-fold to the center and 2.2-fold to the reference.While the second dominant group,Prochlorococcus,had about 50%increasing biomass at the edge relative to reference,and was mediate at the center.Diatoms biomass was also~2.5-fold at the edge compared to the center and the reference.Diatoms could be responsible for the~50%enhancement in bSiO2 flux at the center through lateral transport from the edge.The positive correlation between POC flux and haptophytes_8 biomass at the edge implied their importance in particles export.Be same as the ACEs,the edge modulating in the Rossby eddy had also been observed.But it was different in the biogeochemical process as the penetrating of the Kuroshio Current into the northern SCS altered the phytoplankton community structure,so did the efficiency of the biological pump.