Currently, the spatiotemporal distribution patterns and community assembly mechanisms of microzooplankton from the continental shelf to the deep-sea basin remain largely understudied. In this study, we investigated the distribution characteristics and driving factors of ciliate communities in the northeastern South China Sea during summer and winter. The results showed that ciliate α‑diversity was generally similar between the two seasons, but community composition exhibited significant seasonal differences. Spatially, α‑diversity decreased significantly from shallow to deep waters, while community composition differences were mainly observed between the upper and deeper water layers. The driving mechanisms of community assembly were scale‑dependent: at the overall community level, environmental factors explained more of the community variation than spatiotemporal factors, with physical environmental factors playing a dominant role, likely due to the complex physical oceanographic processes in the study area. Within the three spatial sub‑regions, seasonal effects had a significantly stronger influence on the communities than other factors. Network analysis revealed that ciliates had more associations with phytoplankton than with environmental factors; diatoms and physical environmental factors dominated the co‑occurrence network among ciliates, phytoplankton, and the environment, indicating that both play important regulatory roles in the community stability of the microbial food web. This study deepens our scientific understanding of the spatiotemporal assembly mechanisms of microzooplankton in open ocean ecosystems.