The biological carbon pump (BCP) is a key mechanism sustaining the ocean’s carbon sink and plays a crucial role in the global carbon cycle. However, systematic understanding of the multi-process regulation of the BCP remains limited, with critical knowledge gaps in marginal seas and the twilight zone, insufficient research on heterotrophic processes, and poorly constrained physical-biological coupling mechanisms. We systematically investigated the regulatory mechanisms of the BCP in Chinese marginal seas following the core framework of “carbon fixation-carbon export-carbon consumption”. This review summarizes our recent advances achieved in this field. For carbon fixation, we revealed the spatiotemporal evolution of nutritional strategies of mixotrophic phytoplankton through multi-scale environmental gradient studies spanning estuaries, continental shelves, and ocean basins. For carbon export, we focused on novel non-gravitational export pathways, quantitatively constraining the contributions and governing mechanisms of the physically driven mixed-layer pump and zooplankton vertical migration. For carbon consumption, we quantify heterotrophic remineralization across the euphotic and twilight zones and resolve its microbial metabolic regulation. By establishing a full-water-column systematic research framework, this study elucidates the multi-process regulation mechanisms of the BCP in Chinese marginal seas, advancing understanding of ocean BCP processes and improving the predictive accuracy of key carbon fluxes. We further identify critical directions for future BCP research that require breakthroughs in cross-scale expansion, multi-source data integration, and three-dimensional observation system development.