Abstract: Based on the phytoplankton and environment data collected from the deep-water cage aquaculture area of Houshui bay and its adjacent waters between April 2018 and January 2019, this paper analyzed the seasonal variation of phytoplankton community and its relationship with environmental factors, as well as the impact of deep-water cage aquaculture on the environment. In this research, 214 phytoplankton taxa were identified, which belonged to five phyla and 65 genera, with Bacillariophyta being the main group. The dominant species were Skeletonema costatum, Pseudo-nitzschia delicatissima, Skeletonema tropicum, Thalassiosira subtilis and so on. There were obvious seasonal variations in species composition of the dominant. The phytoplankton abundances and the biodiversity indices (Margalef richness index, Shannon-Wiener diversity and Pielou evenness) were significantly different in season, and they were generally higher in summer and autumn than in winter and spring. The results of Bray-Curtis analysis and non-metric multidimensional scaling analysis showed that the composition of phytoplankton community had significant seasonal differences, but there was no significant difference between the aquaculture area and the control point. Redundancy analysis suggested that the main factors affecting the community structure were temperature, salinity, nutrition, and various phytoplankton respond to these main factors in different ways. The water quality of Houshui bay was fine during the investigation. There was no significant difference in phytoplankton community composition and environmental factors between the aquaculture areas and the control points in each season. Deep-water cage culture had no significant effect on the water quality and phytoplankton in Houshui bay.