Abstract: Based on four cruise surveys carried out from 2013 to 2014, we analyzed phytoplankton community structure and seasonal pattern and compared them with those of the adjacent sea area. We also assessed the relationship between phytoplankton and environmental factors and potential influence by the second phase of the Xiamen Airport Project construction on phytoplankton. A total of 82 species (excluding unknown taxa) belonging to 43 genera of 3 classes were identified from 95 samples, in which diatoms were dominant in both the species composition and the abundance. Dinoflagellates was the second-largest group. Cyanobacteria was the least with only one species. Signifi-cant seasonal changes existed for phytoplankton species composition and abundance. Species richness was the lowest in March and the highest in November. The annual average phytoplankton abundance was 47.09×10³ cells/L with the peak in January and the minimum in November. The dominant species were diatoms including thirteen species: Guinardia delicatula, Ecampia zoodicaus, Skeletonema spp., Paralia sulcata, Thalassiosira exigua, Asterionella notula, Chaetoceros curvisetus, Nitzchia closterium, Bacillaria paradoxa, Chaetoceros abmormis, Leptocylindrus minutum, Pleuro-sigma angulatum and Pleurosigma formosum. In detail, Paralia sulcata and Skeletonema spp. were dominant species in four seasons. Shannon-wiener diversity index and Pielou’s evenness index indicated a more integrated and stable state of phytoplankton community. Compared with adjacent sea areas around Xiamen Island, the Northern Jinmen Island had medium level of richness of phytoplankton species, similar species composition but different dominant species and higher abundance. Pearson Correlation Analysis indicated that phytoplankton abundance was remarkably nega-tively associated with water temperature in November and was significantly negatively linked with salinity in January and November. Phytoplankton abundance were correlated positively to suspended substance in January but negatively linked in July. The phosphate and dissolved inorganic nitrogen were significantly positively linked with phytoplankton abundance in January. Chlorophyll a content was positively associated with phytoplankton abundance in November and significantly positive in January. Phytoplankton abundance in March was not clearly related to environmental factors. The second phase of Xiamen Airport Project mainly affected phytoplankton by massive suspended substance and shock wave during construction period. Moreover, ocean engineering cases indicated that phytoplankton abundance of investi-gated water began to rise and the disorder of dominants succession gradually recovered to the pre-construction status. More investigations of phytoplankton after completing ocean engineering projects are required to assess ecological affect by the second phase of Xiamen Airport Project.