The levels and depth distributions of As, Cd, Cu, Zn, Pb, Hg, Fe and Mn in two sediment cores DY2 and DY4 collected from the “Cattle Pond” of Dongdao Island, South China Sea, were determined and analyzed with the main objective to identify the sources of these elements and evaluate the corresponding sedimentological and geochemical processes. Lithological characters and sedimentary parameters such as LOI950°C, CaO, LOI550°C and TOC indicate that the depth of 96 cm and 87 cm are the critical points for DY2 and DY4 cores, respectively. As, Cd, Cu, Zn, Hg and P are remarkably enriched in the ornithogenic sediments above the critical depth points; their concentration-versus-depth profiles are similar to those of TOC and LOI550°C; the ratios of As, Cd, Cu, Zn, Hg over Ca are significantly correlated with P/Ca. Statistical and comparative analyses of these elements’ levels in the ornithogenic sediments of DY2 and DY4 strongly suggest that seabird droppings are the main source of these elements. Additionally, for the upper sediment layers of DY2 and DY4 cores, Fe oxide sorption mechanism, like organic matter, may also play an important role in the abundances of heavy metals. Heavy metal Pb has geochemical characteristics distinctly different from those of As, Cd, Cu, Zn, Hg and P, and its isotope composition indicates an origin of anthropogenic emissions from the surrounding countries. These geochemical characteristics in the orinithogenic sediments of Xisha Islands are compared with the studies in the remote Antarctic and Arctic regions.