Coastal hypoxia, exacerbated by the combined influence of eutrophication and global warming, presents a significant environmental challenge. However, the lag correlation between organic matter (OM) export from the upper layers and bottom dissolved oxygen (DOBOT) reduction still lack clear elucidation. This study investigated the coupling between net ecosystem production (NEP, representing the maximum OM export) and DOBOT in the Changjiang River plume (CRP), using a wave-driven profiler system. The high-resolution profiles revealed rhythmic fluctuations in water column NEP, with sediment-water exchange (−74.6%) and NEP (−4.0%) dominating DOBOT reduction. Notably, surface NEP impacts DOBOT with a lag time of 25.65 h, indicating an OM sinking speed of 1.32 mm s−1. NEP at a depth of 3.4 m exerted the most significant influence on DOBOT, explaining a 12% reduction. These findings elucidate the response mechanism of DOBOT reduction to upper OM export and provide insights for hypoxia prediction in coastal and estuarine areas.