Planktonic ciliates are important components of microzooplankton in marine pelagic ecosystems. However, the study of planktonic ciliate distribution in different water masses of the Southern Ocean was scarce. We investigated planktonic ciliate distribution in different water masses of the Cosmonaut and Cooperation Seas during December 6, 2019 to January 6, 2020. Tintinnids contributed 5.97% and 3.65% to total planktonic ciliate abundance and biomass, respectively. Both total planktonic ciliate and aloricate ciliate abundances were highest in the Winter Water (WW), while tintinnid abundance was highest in the Summer Surface Water (SSW). The biomasses of total planktonic ciliates and aloricate ciliates were highest in SSW, while that of tintinnids was highest in WW. The lowest values were all observed in the Circumpolar Deep Water (CDW). Fourteen tintinnid species were grouped into three types based on their distribution characteristics: Type I (Amphorellopsis quinquealata, Codonellopsis gaussi, Cymatocylis antarctica, Cymatocylis cf. calyciformis, Cymatocylis cf. convallaria, Salpingella faurei, and Salpingella sp.) species distributed in all the water masses; Type II species (Cymatocylis cf. cristallina, Cymatocylis cf. drygalskii, and Laackmanniella naviculaefera) were found in SSW and WW; and Type III species (Amphorides laackmanni, S. costata, S. laackmanni, and one undefined species) were restricted to WW and CDW. Our results characterize the distribution patterns and influencing factors of planktonic ciliates in different water masses in the Cosmonaut and Cooperation Seas, which will be helpful to understand the pelagic assemblage variation and constitute a baseline for studying the marine food web variation in the Antarctic Zone of the Southern Ocean.