Mesoscale eddies, which contribute to long-distance water mass transport and biogeochemical budget in the upper ocean, have recently been taken into assessment of the deep-sea hydrodynamic variability. However, how such eddies influence sediment movement in the deepwater environment has not been explored. Here for the first time we observed deep-sea sediment transport processes driven by mesoscale eddies in the northern South China Sea via a full-water column mooring system located at 2100 m water depth. Two southwestward propagating, deep-reaching anticyclonic eddies passed by the study site during January to March 2012 and November 2012 to January 2013, respectively. Our multiple moored instruments recorded simultaneous or lagging enhancement of suspended sediment concentration with full-water column velocity and temperature anomalies. We interpret these suspended sediments to have been trapped and transported from the southwest of Taiwan by the mesoscale eddies. The net near-bottom southwestward sediment transport by the two events is estimated up to one million tons. Our study highlights the significance of surface-generated mesoscale eddies on the deepwater sedimentary dynamic process.