The plankton assemblages are mainly composed by phytoplankton and zooplankton communities, which are both crucial in the lacustrine ecosystems. It is well known about their biodiversity and composition structures; however, limited knowledge on their nestedness and interspecific interactions. In the East Lake Taihu, this study investigated the nestedness and interaction characteristics of phytoplankton and zooplankton communities in 2019-2020, by applying the appearance-absence matrix and bipartite model. The results showed: (1) The physicochemical characteristics were similar among spring, autumn and winter, but are significantly different in summer. Meanwhile, the comprehensive pollutant index was clearly higher in the southwest than that in the northeast. (2) The nestedness pattern induced by environmental heterogeneity for the phytoplankton communities indicated their compositions in autumn and winter were subset of those in spring and summer. By contrast, the zooplankton communities did not demonstrate such pattern. (3) The biotic interactions of plankton assemblies differed seasonally. The bipartite network was more complex in spring, summer, and autumn than that in winter. Moreover, the winter plankton had the fiercer competition, the higher specialization, the lower generality and higher vulnerability than other seasons did, which suggested a less stable network. Ultimately, niche separation caused by temporal-spatial differences of aquatic environment in the East Lake Taihu may be responsible for the seasonal differences of plankton assemblages' nestedness and bipartite networks.