Upwelling system in western Taiwan Strait is important for facilitating the fishery production. This study investigated hydro-chemical properties, phytoplankton biomass, phytoplankton species composition, three-dimensional (horizontal, vertical and transect) distribution of phytoplankton abundance, as well as phytoplankton annual variation and the correlation of phytoplankton community with the upwelling of underlying current and nutrients according to samples of Fujian-Guangdong coastal upwelling zone in western Taiwan Strait from August 27 to September 8, 2009. The results manifest that the nutrient-rich cold and high salinity current on the continental shelf of South China Sea upwells to the Fujian-Guangdong coastal waters through Taiwan Bank and the surging strength to surface is weak while strong at 30-m layer. The thermohaline center of coastal upwelling shifts to the east of Dongshan Island and expanded to offshore waters in comparison with previous records. A total of 137 phytoplankton species belonging to 59 genera in 4 phyla are identified excluding the unidentified species. Diatom is the first major group and followed by dinoflagellate. Cyanobacteria mainly composed by three Trichodesmium species account for a certain proportions, while Chrysophyta are only found in offshore waters. The dominant species include Thalassionema nitzschioides, Pseudo-nitzschia pungens, Thalassionema frauenfeldii, Pseudo-nitzschia delicatissima, Rhizosolenia styliformis, Chaetoceros curvisetus, Diplopsalis lenticula and Trichodesmium thiebautii. Phytoplankton community mainly consists of eurythermal and eurytopic species, followed by warm-water species, tropic high-salinity species and oceanic eurythermic species in order. Phytoplankton abundance ranges from 1.00×102 ind./L~437.22×102 ind./L with an average of 47.36×102 ind./L. For vertical distribution, maximum abundance is found at 30m-depth and the surface comes second. Besides, the abundance below 30m decreases with increasing water depth. The horizontal and transect distribution of phytoplankton abundance are both displayed in patchy size, and the peak area is the offshore waters from the east of Dongshan Island to the south of Zhangpu which is basically coincident with the thermohaline center of the upwelling, but the distribution range of phytoplankton high abundance is expanded out of the upwelling center. Phytoplankton abundances on 3 transects in offshore waters from the east of Dongshan Island to the south of Zhangpu are higher than that of nearshore waters and the other 5 transects. Moreover, the underlying current is accompanied by shade flora so as to offer a certain evidence for the presence of upwelling. Phytoplankton abundance at 30m-depth and bottom both present low significant positive correlation with phosphate, while there are not significant correlations between the content of inorganic nitrogen and phytoplankton abundance in all water layers. The intensity and range of Fujian-guangdong coastal upwelling has a regulating effect on the species succession, abundance distribution and the location of phytoplankton peak area.