Abstract: Deep ventilation processes in the Northwest Pacific play a critical role in regulating global climate change and the carbon cycle. Radiolarians, as typical environmental indicator in subpolar regions, serves as an important tool for reconstructing the evolution of deep ventilation in the Northwest Pacific. A thorough understanding of radiolarian environmental implication is prerequisite to accurately interpreting past changes in radiolarian assemblages. This study compares the differences in radiolarian assemblage composition results from two pretreatment methods (63 µm sieving and natural settling technique) applied to the same sediment core retrieved from the Japan Sea (also known as the East Sea). Additionally, the reliability of radiolarian-based proxy is evaluated using morphometric analysis of characteristic species and species group. Our results reveal systematic discrepancies between the two pretreatment methods. The 63 µm sieving method yields higher relative abundances of warm-water species compared to natural settling, while the relative abundances of Cycladophora davisiana and Lithomelissa setosa are significantly lower. Moreover, the total absolute abundance of radiolarians and the absolute abundances of characteristic species are consistently lower in the sieved samples than in those processed via natural settling technique. Notably, L. setosa, an indicator of coastal environments, is nearly absent in the 63 µm sieved samples due to its "slender-high" morphology, which is poorly retained by this method. These findings highlight the necessity of using consistent pretreatment methods when comparing and assimilating published radiolarian data in future studies. Furthermore, by systematically comparing the spatial and water depth distribution patterns of C. davisiana in surface sediment samples across the Okhotsk Sea basin, this study demonstrates that pretreatment methods significantly influence the spatial distribution characteristics of this species, whereas its water depth distribution remains consistent. Radiolarian morphometric parameters not only offer a potential quantitative approach for marine micropaleontological research but also hold promise for providing more robust evidence to reconstruct the evolution of intermediate-water ventilation in the Northwest Pacific since the Last Glacial Maximum.