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To further understand the effect of Kuroshio intrusion on phytoplankton community structure in the northeast South China Sea (NSCS, 14°–23°N, 114°–124°E), one targeted cruise was carried out from July to August, 2017. A total of 79 genera and 287 species were identified, mainly including Bacillariophyta (129 species), Pyrrophyta (150 species), Cyanophyta (4 species), Chrysophyta (3 species) and Haptophyta (1 species). The average abundance of phytoplankton was 2.14×103 cells/L, and Cyanobacterium was dominant species accounting for 86.84％ of total phytoplankton abundance. The abundance and distribution of dominant Cyanobacterium were obviously various along the flow of the Kuroshio, indicating the Cyanobacterium was profoundly influenced by the physical process of the Kuroshio. Therefore, Cyanobacterium could be used to indicate the influence of Kuroshio intrusion. In addition, the key controlling factors of the phytoplankton community were nitrogen, silicate, phosphate and temperature, according to Canonical Correspondence Analysis. However, the variability of these chemical parameters in the study water was similarly induced by the physical process of circulations. Based on the cluster analysis, the similarity of phytoplankton community is surprisingly divided by the regional influence of the Kuroshio intrusion, which indicated Kuroshio intrusion regulates phytoplankton community in the NSCS.