Two cruises were carried out in the northern South China Sea (18°-23.5°N、109°-120°E) in summer (19^th July to 16^th August, 2009) and winter (6^th to 30^th January, 2010). Phytoplankton samples were analyzed and 150 taxa belonging to 72 genera of 4 classes were identified by Utermöhl method in summer samples. The cell abundance of phytoplankton ranged 0.16-6001.78×10³ cells/L, the average cell abundance was 26.49×10³ cells/L, in which Bacillariophyta accounted for 25.81×10³ cells/L. The dominant species in summer were Trichodesmium thiebautii、Thalassionema nitzschioides、Pseudo-nitzschia delicatissima and Gymnodinium spp. etc. 168 taxa belonging to 58 genera of 4 classes were identified in winter samples, the cell abundance of phytoplankton ranged 0.08-37.52×10³ cells/L, the average cell abundance was 2.69×10³ cells/L, in which Bacillariophyta abundance was 2.49×10³ cells/L. The dominant species in winter were Thalassionema nitzschioides, Thalassionema frauenfeldii and Chaetoceros messanensis, etc. The average cell abundance of phytoplankton in the 5m layers reduced rapidly from coastal zone to open sea in summer, and a high abundance value of phytoplankton occurred in coastal seawaters of east of Guangdong Province and east of Hainan Provence, while a high value of phytoplankton cell abundance occurred in Pearl River Estuary and sea basin in winter. In general, phytoplankton cell abundance was lower at deep-water stations (>200m) than at shallow water stations (<200m) during this two cruises. The average cell abundance of phytoplankton in summer was higher, but species richness was lower than that in winter. The average Shannon-Wiener diversity index of phytoplankton community were 2.12 and 2.36 in this two cruises, average Pielou index were 0.79 and 0.81, respectively. Pearson Correlate Analysis of phytoplankton cell abundance with environmental factors showed that the phytoplankton cell abundance correlated negatively (in 0.01 level) to the salinity in this two cruises and negatively correlated (in 0.01 level) to phosphate concentration in winter.