This dataset includes the total mass flux (TMF, mg m-2 d-1), particulate organic carbon (POC) content (%), POC flux (mg C m-2 d-1), fecal pellet numerical flux (pellets m-2 d-1), and fecal pellet carbon (FPC) flux (mg C m-2 d-1) of time-series sediment trap samples at 500 m and 2190 m water depths of the mooring TJ-T in the southern South China Sea from June 2020 to May 2021. A total of 42 samples were obtained (21 samples from each water depth) for this dataset. TMF of sediment trap samples was derived when the dry weight (mg) was divided by the collecting area (0.5 m2) and collecting time (16 days). POC content of sediment trap samples was measured by a Cario EL Cube elemental analyzer at the Third Institute of Oceanography, Ministry of Natural Resources, with a precision of better than ±0.02% (SD, 1σ; n = 2). POC flux was calculated by the product of the TMF and POC content. Zooplankton fecal pellets in the sinking particles were observed under a Leica M125 stereomicroscope coupled to a Leica digital camera at the State Key Laboratory of Marine Geology, Tongji University. Fecal pellets were identified, counted, and measured according to three shapes: ellipsoidal, cylindrical, and spherical, and each shape was counted and measured separately using the Fiji software. The biovolumes of the first 50–100 pellets were calculated using formulas for each shape, and the biovolume-carbon content conversion factor used is 0.036 mg C mm-3 for all pellets. Fecal pellet numerical and carbon fluxes were obtained when the pellet number and carbon content were divided by the collecting area (0.5 m2) and collecting time (16 days).