Deep-sea profile observations are the key to deciphering the vertical distribution of life activities and quantifying the efficiency of the “biological pump”, yet such data remain scarce. In this study, we used a Maxi Multinet Plankton Sampler to collect biological samples from nine continuous depth layers across a 4000 m profile on both sides of the Eauripik Rise in the Caroline Basin. Using on-site fixation, Rose Bengal staining, morphological identification, and statistical analysis, we quantitatively characterized the full-depth gradient succession of siliceous radiolarians and their environmental controls. Our results show that the total radiolarian abundance peaked at 0–100 m and decreased with increasing depth on both stations. Heatmap analysis based on species presence–absence data revealed that temperature controlled the vertical distribution succession of radiolarians, with distinct thermal niche differentiation from the surface to deep waters. Four depth-stratified species assemblages indicative of water mass environments were identified based on critical temperature thresholds of 24°C, 8°C, and 1.8°C: Didymocyrtis tetrathalamus and Tetrapyle group as warm mixed layer species (>24°C, 0–200 m); Larcopyle buetschlii as thermocline species (8–24°C, 100–500 m); Cladoscenium ancoratum, Larcopyle weddellium, Cycladophora cf. davisiana, and Saturnalis circularis as low-temperature species (1.8–8°C, 500–2400 m); and Thecosphaera melitomma, Axoprunum octatignum, and Druppatractus hastatus as cold-water species (<1.8°C, 2400–4000 m). Cluster analysis indicated that the community structures differed between the two sides of the Eauripik Rise, largely due to an uneven distribution of Antarctic Circumpolar Deep Water caused by topographic barrier effects. Above the ridge, however, communities exhibited a three-layer vertical structure with strong connectivity within each layer, consistent with the connectivity of the upper and intermediate currents in the East and West Caroline Basins. These findings provide observational data and scientific support for understanding the vertical adaptation strategies of marine organisms and biogeochemical cycling in tropical waters.