Based on the survey of surface sediment in Xiamen Bay in October 2011, the speciation, distribution, and potential ecological risk assessment of heavy metals (Cu, Pb, Zn, Cd, and Cr) in this area were studied us-ing the sequential extraction method and ecological risk assessment method. The results indicated:(1) the total concentrations of these heavy metals were influenced by runoff, industrial wastewater, and sewage, and were all higher in the coastal area than the offshore area while the highest area of Pb was a little far-ther away from the coastal water due to atmosphere deposition;(2) sequential extractions suggested that Cu was mainly composed with residual and Fe/Mn-oxide bound fractions, Pb was bound to Fe/Mn-oxide, Zn and Cr were dominated by residual, and Cd bound to exchangeable and carbonate fractions; (3) the order of migration and transformation sequence was Cd>Pb>Cu>Zn>Cr and the degree of pollution was Cd>Pb>Cu>Zn>Cr;and (4) the ratios of the secondary and primary phases showed that Zn and Cr were both clean, Cu may be polluted, Pb was moderately polluted, while Cd was heavily polluted.