Display omitted •Cell cluster removal device based on spiral inertial microfluidics.•Cell cluster removal with high volumetric throughput, removal efficiency, and biocompatibility.•The first demonstration of the selective removal of large CHO cell clusters from bioreactors using microfluidics.•The first report on the large-particle trapping effect in spiral inertial microfluidic devices. Suspension cultures of Chinese hamster ovary (CHO) cells are extensively employed in biopharmaceutical production. During cultivation, CHO cell clusters often form due to cell death and other irregularities, substantially reducing cell growth and productivity. In this study, we introduce a novel method for the selective removal of large CHO cell clusters from bioreactors, utilizing the large-particle trapping effect in spiral inertial microfluidics. A single spiral inertial microfluidic device effectively removed large clusters from CHO cell culture, demonstrating high volumetric throughput, removal efficiency, and biocompatibility. This straightforward, agent-free, and continuous-flow approach can be applied to remove large mammalian cell clusters across various scales and modes of operation (discontinuous or continuous) during cell line development, bioprocess optimization, and biomanufacturing.