<p>Coastal hypoxic zones are expanding globally due to climate change and anthropogenic pressures, posing a serious threat to marine ecosystem health. Extratropical cyclones (ETCs) are key drivers of hydro-biogeochemical variability in the China’s coastal seas, yet their role in modulating near-bottom hypoxia remains poorly understood. Here, we present a 76-hour ship-based time-series observation in the North Yellow Sea (NYS) during an ETC passage, integrating atmospheric forcing, hydrodynamics, and suspended particle size distribution data to resolve the underlying mechanisms. We found that in NYS near the Shandong Peninsula, wind-driven vertical mixing alone was insufficient to erode the seasonal pycnocline and ventilate hypoxic bottom waters. Instead, ETC-induced Ekman transport intensified the barotropic pressure gradient between the Bohai Sea and NYS, driving a transient coastal current during the cyclone’s decay phase that advected oxygen-rich, well-mixed waters into the hypoxic zone. Particle dynamics revealed that optimal light and nutrient conditions near the pycnocline enhanced phytoplankton growth and biological flocculation, producing large, fast-settling flocs that significantly increased the export of organic matter. This, in turn, intensified bottom hypoxia through subsequent microbial decomposition—a process that was suppressed after the ETC due to pycnocline deepening and weakened stratification. This study provides the first field-based evidence for the dual role of ETCs in both alleviating hypoxia through coastal currents and reducing flocculation-driven organic matter (carbon) export. Given the observed decline in summer ETC frequency and intensity in China’s coastal seas under recent climate trends, our findings suggest an increased risk of more persistent and widespread hypoxia, alongside enhanced carbon sequestration, underscoring the need for high-resolution monitoring and predictive modeling to safeguard marine ecosystem health.</p>