A topography change in the continental plain plays an important role in nutrient replenishment mechanisms in oligotrophic oceans. Effects of the topography on the nutrient distribution in the western South China Sea (WSCS) have been overlooked since most studies have focused on the dipole-induced upwelling and downwelling processes of nutrients. We hypothesize that the seamount topography in the northwestern side of the WSCS contributes to the upward distribution of nutrients. We conducted a cruise to investigate the vertical distribution of nutrients in a large area where there is a gradient in the topography: shallow in the north to deep in the south. Our results showed that the depth contours of nutrients, temperature, and salinity shoaled upward from deep to shallow with their isolines being parallel to the bottom depth. The depth of mixed layer, pycnocline, nutricline, and deep chlorophyll maximum showed the similar topographic effect. In the deep water column of 4,308 m deep, integrated NO and PO over 0–200 m were 879.60 and 81.78 mmol m, but increased to 2010.17 and 143.79 mmol m in the shallow water column of 930 m deep, respectively. The increased supply of nutrients enhanced 0–200 m integrated chlorophyll from 21.71 mg m in the deep water column to 51.51 mg m in the shallow water column. These results demonstrate that topographic elevations such as seamounts induce deep-to-shallow shoaling and upwelling that lead to enhanced nutrients and biological production in the euphotic zone of oligotrophic oceans.