Seamounts are ubiquitous features in the world ocean with potential for increasing plankton biodiversity and abundance, and providing important habitats for aquatic predators. Although ecological importance of seamount is well known, the mechanisms for supporting seamount-associated microzooplankton (e.g., pelagic ciliates) communities remains to be substantiated. In this study, pelagic ciliate community structure variations and their relationship with environmental variables were investigated in the Caroline seamount in late (2017) and early summer (2019). Above the seamount in 2019, ciliates exhibited higher abundance and biomass than off the seamount, which supported the classic hypothesis of seamount effect. Aloricate ciliate small size-fraction (10–20 μm) was dominant in bathypelagic (>1000 m) zone. Although relative abundance of small size-fraction was similar in both 2017 and 2019, the absolute abundance in 2019 seamount-effect stations were obviously higher than that in 2017. All abundant tintinnids were classified into surface- and DCM (deep Chl a maximum layer)-peak groups. Among them, four abundant tintinnids (Acanthostomella conicoides, Eutintinnus hasleae, Salpingella curta and S. minutissima) had higher abundance at DCM and might uplifted to shallower waters by upwelling at 2019 seamount-effect stations. The multivariate biota-environment analysis showed that environmental variables have significant impacts on the ciliate community structures in 2017 and 2019. Higher Chl a and nutrient concentrations, and sustained upwelling might be two potential mechanisms for microzooplankton seamount effect. Our study constitutes a rather solid foundation for quantitative and functional study of microzooplankton populations over oligotrophic tropical seamounts.