Coastal depositional systems play a crucial role in the sequestration of terrigenous organic carbon (OC), especially deltas and coastal mud belts, which are two of the most efficient OC burial hotspots. Investigation into long-term coastal OC burial is challenging since the analysis of modern coastal environments only provides a snapshot of OC burial. Marine Isotope Stage 3 (MIS 3) refers to a unique interval in the last glacial period, characterized by a protracted falling sea level punctuated by millennial-scale climate oscillations. The study of OC burial during MIS 3 can help to estimate and predict changes in coastal OC burial driven by sea-level oscillations and extreme climate events. Here, we target late MIS 3 strata beneath the southern East China Sea. Based on the analysis of total organic carbon, total nitrogen content, stable organic carbon isotopic composition, and major and trace elements, this study demonstrates that relative sea-level changes control sediment provenance and sedimentary processes in coastal environments, which in turn regulate coastal OC burial during the late MIS 3. The burial of OC in the coastal ocean during MIS 3 deviates from the typical expectation that carbon burial is facilitated during transgression or high sea-level periods. Sediments deposited during high sea-level periods in late MIS 3 exhibit the lowest OC burial flux and contents due to long-distance transport from distant sources. The study highlights that the highest burial flux and contents of OC were found in deposits preserved during sea-level lowstands. This indicates that short-distance transport, local sources, and mountainous rivers affected by the monsoon and experience frequent floods, are associated with the highest OC burial and contents. Short and rapid climate warming events likely contribute to OC burial in late MIS 3 by intensifying precipitation and nutrient-rich supplies, thereby increasing the input of terrestrial and marine OC. This observation is noteworthy as it challenges the conventional understanding of the relationship between sea level and carbon burial. The study of OC burial in late MIS 3 is helpful in understanding how OC burial reacts to sea level oscillations and rapid climate warming events.