Time-series samples intercepted via three synchronized moored sediment traps, deployed at 1000 m, 2150 m, and 3200 m in the northern South China Sea (NSCS) during June 2009–May 2010, were analyzed to quantify the bioactive trace metal fluxes in sinking particles and investigate their different source contributions. Iron (Fe) primarily originated from lithogenic sources. Manganese (Mn), cobalt (Co), nickel (Ni), copper (Cu), and zinc (Zn) exhibited various degrees of enrichment over their continental crustal ratios. Since the sources of bioactive trace metals in sinking particles can be divided into lithogenic, biogenic, and excess fractions, mass conservation calculations were used to quantify the contribution of each source. The results showed that Fe, Mn, and Co had extremely low biogenic proportions (0.1–3.3%), while Ni, Cu, and Zn had higher proportions (2.7–17.3%), with the biogenic fraction decreasing with the depth. Moreover, excess sources accounted for a significant proportion of Mn (68–75%), Co (34–54%), Ni (60–62%), Cu (59–74%), and Zn (56–65%) in sinking particles at the three sampling depths. The excess fractions of Mn, Co, and Cu in sinking particles can be affected by authigenic particles. This is supported by their similar scavenging-type behavior, as observed via the increase in their fluxes and enrichment patterns with the increasing depth. Furthermore, the excess fractions of Ni, Cu, and Zn may have significant contributions from anthropogenic sources. The variability of Fe in sinking particles was mainly controlled via lithogenic matter. Notably, organic matter and opal were found to be pivotal carriers in the export of excess bioactive trace metals (Mn, Co, Ni, and Cu) via the water column, accompanied with the elevated ballast effect of lithogenic matter with the depth. However, the transportation of excess Zn was more complicated due to the intricate processes involved in Zn dynamics. These findings contribute to our understanding of the sources and transport mechanisms of bioactive trace metals in the marine environment.