Seabird subfossils were collected on three islands of the Xisha Archipelago, South China Sea. Via elemental analysis, we identified that bird guano was a significant source for heavy metals Cu, Zn, and Hg. Cu and Zn levels in these guano samples are comparable to their levels in wildbird feces, but guano Hg was lower than previously reported. Trophic positions significantly impacted transfer efficiency of heavy metals by seabirds. Despite of a common source, trace elements, as well as stable isotopes (i.e., guano δ(13)C and collagen δ(15)N), showed island-specific characteristics. Bird subfossils on larger island had relatively greater metal concentrations and revealed higher trophic positions. Partition of element and isotope levels among the islands suggested that transfer efficacy of seabirds on different islands was different, and bird species were probably unevenly distributed among the islets. Island area is possibly a driving factor for distributions of seabird species.