In the Southern Ocean, rapid environmental changes (warming, freshening, and poleward shifts of the physiological fronts) are underway. These changes affect the distribution, abundance, and life cycle of protists. However, the spatial distribution of protists is not well understood in the eastern Indian sector of the Southern Ocean. We, therefore, evaluated the effects of environmental factors at the community level (abundance and species composition) and species-specific level (life cycle in diatoms) based on field sampling during the austral summer of 2018/2019. High chlorophyll levels and protist cell densities were observed in the eastern area from 120°E, in contrast to the distribution reported in the 1996 BROKE (The Baseline Research on Oceanography, Krill and the Environment) survey. This inter-annual variation was caused by differences in the sampling periods, nutrients, and zooplankton grazing pressures. North–south variation in protist abundance was well explained by silicate distribution, whereas sea ice variation did not influence it explicitly. The clustering of protist groups was well associated with nutrients, but locally, offshore groups were extended southward by currents and eddies. The cell size of the two dominant Fragilariopsis curta and F. kerguelensis exhibited similar significant relationships with sea ice variation and decreased 60 days after sea ice melted. Our findings demonstrate that sea ice changes do not clearly affect the protist community level but potentially affect the life cycle level of diatoms.