We present isotope ratios of Ni (δ⁶⁰Ni) and Cu (δ⁶⁵Cu) in sinking particles, aerosols, and seawater collected from the northern South China Sea to identify sources and transformation processes of the two metals. In aerosols, δ⁶⁰Ni values are in the range +0.05‰ to +0.56‰, and δ⁶⁵Cu values are in the range −0.33‰ to +0.83‰. The isotope ratios are different from those of lithogenic materials, indicating that the aerosols are anthropogenic in origin. In sinking particles collected at depths of 2000 and 3500 m, δ⁶⁰Ni values are in the range +0.01‰ to +0.54‰ at 2000 m and −0.18‰ to +0.54‰ at 3500 m, and the values exhibit similar temporal variation pattern between 2000 and 3500 m. Based on the significant correlation between δ⁶⁰Ni and the ratio of P/Ni or organic-C/Ni, we hypothesize that the main sources of Ni in the sinking particles originate from both resuspended marine sediments off southwest Taiwan, and biogenic organic particles. The δ⁶⁰Ni in biogenic particles is estimated to be +0.6‰ to +1.0‰, which is 0.3–0.7‰ lighter than that of dissolved Ni in seawater. The isotope ratios of Cu in sinking particles are fairly constant (+0.13‰ to +0.36‰), and the range is between those of marine sediments and labile fractions of marine particles. Thus, Cu in sinking particles is likely to be from marine sediments and biogenic organic particles. Compared with Ni, the correlation between Cu and P or organic-C is weaker, suggesting that the Cu/P and Cu/organic-C ratios are not constant in organic matter or there are additional sources of particulate Cu, such as Fe-Mn oxides and anthropogenic aerosols.