The marine biological carbon pump (BCP) constitutes a core mechanism driving net carbon sequestration in the global ocean, yet substantial uncertainties persist in the quantitative estimation of BCP strength and efficiency. This knowledge gap primarily arises from the scarcity of long-term, continuous observations with high spatio-temporal resolution and incomplete understanding of the coupled regulatory effects of multiple environmental forcings. Here, we elucidate the key mechanisms governing the temporal and spatial variability of BCP dynamics across the South China Sea. Based on long-term time-series observations from sediment traps, we resolve the modulations of episodic short-term events, monsoon–cold eddy interactions, and interannual ENSO variability on the magnitude and composition of particulate organic carbon export. Complemented by high-frequency profiling measurements via an integrated multi-biogeochemical sensor system, we further characterize the fine-scale spatial pattern of BCP efficiency across seamount,  highlighting the critical role of zooplankton-fueled efficient organic carbon export pathways in sustaining seamount ecosystem function. Collectively, our multi-scale observational framework and integrated analyses advance the mechanistic understanding of dynamic biological pump processes and their environmental controls. These findings provide pivotal process-level insights and robust observational datasets for improving regional and global ocean carbon sequestration models.