Accurately quantifying the contribution of terrestrial soil organic carbon (SOC) in marine environment is still a challenge. Moreover, reassessing the effect of climate change on SOC variability is necessary, with the increasing variability of El Niño under greenhouse warming. Here, we present new insights from bacterial 3-hydroxy fatty acids (3-OH-FAs) by systematically analyzing the distributions of 3-OH-FA in soils, lake/river sediments and marine sediments, and propose a novel proxy (RIA, the ratio of odd carbon number iso to anteiso 3-OH-FAs) to quantificationally evaluate the contribution of OC from different components. The reliability of the RIA proxy is tested by using a three end-member model and Monte Carlo simulations along a transect from the Yangtze River estuary to the ECS shelf. Then the RIA proxy is applied to a core in the East China Sea covering the past 700 years, and the results reveal that El Niño (La Niña) induced more (less) precipitation and increased (decreased) SOC deposition. This study provides a novel approach for quantifying terrigenous OC inputs and burial in marginal seas and shows the impact of El Niño-Southern Oscillation (ENSO) modes on SOC loss and burial in marginal seas under global warming.