Analysis of abundance and biodiversity of phytoplankton in ballast water which was exchanged in the high seas of the Pacific Ocean for the vessels calling for Yangshan Deepwater Port was conducted to research the risk of phytoplankton invasion. A total of 4 phyla, 18 genera and 29 species (including variants) of phytoplankton were detected in the samples, in which Bacillariophyta dominates the sample results, 72.4% for Bacillariophyta (common with 13 genera and 21 species), 20.7% for Dinoflagellate (common with 3 genera and 6 species), 3.5% for Chlorophyta (common with 1 genus and 1 species) and 3.5% for Cyanophyta (common with 1 genus and 1 species). In all of the 9 ballast water samples surveyed, red tide algae were identified and there was a potential risk of invasive alien species. The abundance of phytoplankton after ballast water exchange in the high seas was much less than that of ballast water exchange in the domestic coastal waters in China. The current ballast water exchange method can reduce the risk of marine organisms invasion while the ballast water treatment system is required to eliminate hidden risks.