Long-term changes of phytoplankton community by water sampling method in Xiagu Sea waters of Xiamen, China, were investigated in this study. Species composition of the phytoplankton community in these waters changed greatly since the 1950s. The numbers of Dinophyta species increased significantly, although Bacillariophyta species are generally dominant. The succession of dominant species in phytoplankton community is obvious:large-size dominant species such as Biddulphia sinensis of the 1950s were gradually replaced by small-size ones such as Cyclotella striata and Nitzschia closterium, and species that still maintain dominant such as Skeletonema costatum are also small ones, leading the whole phytoplankton community of smaller size. Cell density of phytoplankton community increased greatly, among which cell density of the most dominant species Skeletonema costatum have been increasing in exponent function. Margalef index of phytoplankton community decreased, indicating decline of biodiversity of the community, and dominant character of Skeletonema costatum increased. Generally, the structure of the entire phytoplankton community is becoming more and more singular and unstable, which makes the occurrence of red tides more frequent. The succession in the phytoplankton community is related to the long-term changes in marine environment, influenced by human activities and global climate changes, especially the increases of nutrient content.