Abstract: Over three consecutive spring surveys (2007~2009), we have investigated the phytoplankton community structure and its inter-annual changes in Yangmeikeng artificial reef area, Daya Bay, South China Sea. We identified a total of 151 phytoplankton species, among which diatom is the major group. During the three years, the phytoplankton species composition had no significant differene while the dominant species had undergone significant annual succession; the richness had increased significantly, indicating that the artificial fish reef may have promote phytoplankton′s growth. The K-dominance curves show that annual variation of phytoplankton community diversity is obvious (May, 2008 > April, 2007 > May, 2009), which suggests that the phytoplankton community structure is unstable. The cluster and multidimensional scaling analysis (MDS) shows that the eastern, central and western survey stations in the research area tend to cluster together respectively, which indicates that the area could be influenced greatly by current. Additionally, the difference between the reef area and the control area is unobvious, indicating the impact of the artificial reef could spread to the whole survey area due to the area′s small scope. The redundancy analysis (RDA) shows that temperature, depth, salinity and total suspended solids are main environmental factors influencing the phytoplankton density and spatial distribution. In conclusion, the artificial reef may have effect on the research area, but the unstable influence needs longer continuous surveillance.