Abstract: Carbon source is an important factor influencing bioflocs formation and microbial community composition in Penaeus vannamei aquaculture system, and it is important to elucidate the response of microeukaryotic community in both aquaculture water and bioflocs. Here, we used 18S rRNA gene amplicon sequencing to investigate the microeukaryotic community compositions (MECs) and the interaction of microeukaryotes in water and bioflocs under sucrose input condition. We found that sucrose input significantly affect the MECs, especially in the abundance of Ciliophora, Rotifera and Chlorophyta. After 28 days in culture, microeukaryotic community structure was mainly driven by sucrose, dissolved oxygen, nitrite and phosphate. Co-occurrance network analysis showed that sucrose input can enhance the interaction between Heterokonta, Ciliophora and Rotifer, which is benificial for inhibiting the excessive growth of algae. Briefly, these results revealed the successional patterns and interaction of microeukaryotes in aquaculture water and bioflocs, which may provide new insights into the application of bioflocs technology in shrimp culture.