Geochemical characteristics of a 107 cm long sediment profile, collected from Ganquan Island, South China Sea, were analyzed. Based on concentrations of bio-elements (Cu, Zn, Cd, Ba, As, Se, P), 210Pb and AMS14C dating, we reconstructed seabird population of Ganquan Island over the past 2200 years. Seabirds inhabited this island more than 2200 years ago, and their population displayed remarkable fluctuations with two peaks around 2100–1850 yr BP and 900–300 yr BP, respectively. The seabird population change profile on Ganquan Island is similar to that on Dongdao Island over the past 1800 years. We examined the relationship between the seabird population and climate, and found it quite complicated. The seabird population did not reach the maximum during the Medical Warm Period (MWP) with relatively high average temperature; however, it remained near the peak value for about 600 years during the climatic transition period and the Little Ice Age (LIA), indicating that a relatively cool climate is favorable for seabirds on Ganquan Island.