Two transects were designed to study the composition and distribution of ciliates in northern South China Sea during the Open Cruise of Northern South China Sea, CAS. The two transects covered the Pearl River discharge area, the eastern Guangdong upwelling area and the open seas of northern South China Sea. 38 species belonging to 22 genus ciliates were identified, 27 species of 15genus were Tintinnida. 9 species belonging to Tintnnopsis genus were identified, followed Strombidum (5 species). The dominate species was Mesodinium pulex（18.1%），followed by Strombidium tintinnodes (97%) and Tintinnopsis urula (5.8%). Ciliate species number and abundance decreased from coast to offshore, which was similar to the distribution pattern of chlorophyll a. Ciliate species number showed negative relationship with salinity (R2=0.53,P＜0.05), and negative relationship with temperature (R2=0.43,P＜0.05), ciliate species number decreased as temperature increased. No obvious relationship was found between ciliate abundance and temperature or salinity, because high ciliate species number and abundance were found in high salinity upwelling area. Ciliate species number (R2=0.36,P＜0.05) and abundance (R2=0.36,P＜0.05) showed positive relationship with the concentration of chlorophyll a. The Pearl River discharge and the cold upwelling water carried sum nutrients, sustained high phytoplankton biomass, and caused high ciliate species number and abundance, while oligotrohic phenomena prevailed in the open seas of northern south china sea, so ciliate species number and abundance in the open seas were lower than the coast.