The intensity of cyanobacterial blooms that predominate in the world's lakes and reservoirs is variable, which may lead to differing effects on the freshwater ecosystem. Planktonic eukaryotes play key roles in the structure and function of freshwater ecosystems; however, little is known about the influence of cyanobacterial blooms on eukaryotic plankton communities and their function. Herein, the dynamics of eukaryotic plankton communities in Hongze Lake, which is the fourth largest freshwater lake in China, with a range of bloom levels occurred, from low to high, were studied to reveal the effect of cyanobacterial blooms' spatial heterogeneity on planktonic eukaryotes. Results showed that the diversity, richness, and evenness of eukaryotic plankton community were not affected by low level of bloom; however, they were decreased obviously by high level of bloom. Metazoa, Ochrophyta, Chloroplastida, Cryptomonadales, and Ciliophora were the main planktonic eukaryotes in this lake. Metazoa relative abundance declined 25.1% and relative abundance of eukaryotic phytoplankton (mainly Ochrophyta, Chloroplastida, and Cryptomonadales) and Ciliophora increased 17.4% and 2.0%, respectively, during the period with low level of bloom; conversely, the site with the high bloom level manifested the opposite changes. The linkage density of planktonic eukaryotic network was 0.188 and 0.138 with low and high level of bloom, respectively, indicating the stability of planktonic eukaryotes was lower when a high level of bloom occurred compared to that of a low bloom level. Our findings indicate that cyanobacterial blooms should be controlled at low level to avoid their obvious negative impact on microeukaryotes in lakes or reservoirs.