Trenches are the “last front” in marine science research. Fully understanding organic carbon (OC) recycling in the water column is essential to understand the trench sediment being a depocenter of OC.   Here we presented the first synergic study of the dark carbon fixation (DCF) and size-fractionated microbial community respiration proxy (MCRP), along with the distribution of particulate organic carbon (POC) over the entire water depths in the Atacama Trench. Depth profiles of DCF rate at most sites showed a decrease from 5m to 6000 m and went up in hadal trenches indicating the importance of DCF in the dark ocean. MCRP was notably decreased from the epi-to mesopelagic zone (~1000m) and kept constant in bathy- and abyssopelagic zones, but varied in hadalpelagic water significantly from overlying water column, with some extremely high rates in bottom depths. Relatively, over 60% (71.00±12.10%, n=123) of the total MCR has contributed from particle-associated (PA) fractions (>0.8 µm) rather than the free-living (FL) fraction (0.2-0.8 µm). Overall, the dark DCF rates were too little compared to 3 magnitudes higher MCRP to be counted as important energy sources in Atacama Trench. The depth-integrated DCF accounted for as much as 33% of the net primary production estimated from remote sensing, of which the hadalpelagic accounted for 3.0%. This first quantitative exploit of the study will provide a basic understanding of processes in trench storage of POC and marine OC cycling.