The mooring tethered time-series sediment traps (TS-traps) collect sinking particles in the ocean, enabling the estimation of biological pump (BP) efficiency based on the assumption of vertical settling. However, the advection of sea water can disperse particles over long distance during the sinking process, introducing uncertainties into the estimates of BP efficiency. In the South China Sea, mesoscale eddies generate significant lateral transport above the mesopelagic zone, which has a large impact on the collecting area and source funnel of TS-traps. We studied the role of eddies in the lateral transport of sinking particles using a Lagrangian Particle Tracking Model (LPTM) which was forced by three-dimensional currents of eddy composites derived from the global Hybrid Coordinate Ocean Model (HYCOM). The eddy reanalysis using the HYCOM outputs was validated using occurrence, genesis and dissipation statistics of eddies. Backward particle tracking was performed at three stations located in the northern, central and southwestern SCS, respectively. The results indicate that the vertical sinking assumption is invalid when the particle sinking velocity is relatively low. Furthermore, the fraction of surface sources from the edge of the eddies depends on both the sinking velocity and seasonal variability of the background current. The eddy current controls the movement of particles within the eddy, and many of the particles with a sinking velocity <80 m d−1 can be transported from the edge to the eddy center. The source funnel within the mesoscale eddy is tilted vertically, leading to an asymmetrical distribution of the particle source around the trap location. Finally, for slow-sinking particles, trap-collected particles could originate from the subsurface located tens to hundreds of kilometers away from the trap location. Overall, our results highlight the role of mesoscale eddies in interpreting trap measurements.