Ubiquitous mesoscale eddy-front systems are hotspots of carbon export, yet how their decay phase regulates the biological pump in strongly stratified oceans remains unknown. Utilizing ship-based observations from a decaying cyclonic eddy off southeastern Sri Lanka, we reveal that while both the eddy interior and frontal zones exhibit elevated phytoplankton biomass due to different nutrient supply mechanisms, they drive divergent particulate organic carbon (POC) transfer efficiency: enhanced within the eddy but reduced at the front. Subsurface hydrodynamic processes and particle size distributions shaped contrasting export efficiency. During the decay phase, downwelling, weaker stratification, and larger particles inside the eddy promoted efficient POC transfer to depth. Conversely, frontal upwelling, strong stratification induced by water-mass convergence, and finer particles attenuated export. These findings demonstrate that decaying eddy-front systems exhibit spatially heterogeneous carbon sequestration efficiencies, challenging assumptions of uniform attenuation rates and underscoring the need to resolve life-stage dynamics in biological pump assessments.