In order to understand the characteristics of speciation and vertical distribution of heavy metals in the sediments, columnar sediments were collected in surrounding waters of Ma'an Archipelago in June 2018. Seven heavy metals (Cd, Cu, Zn, Pb, Cr, As, Ni) were analyzed, with the improved European Community Bureau of Reference (BCR) method, by measuring the grain size composition of columnar sediments, and the vertical distribution characteristics and sources of heavy metals in the sediment of Ma'an Archipelago, by combining the analyzing method, I_geo, correlation and potential ecological risk index, were explored. The results showed that fine silt (D[3,2]) was dominant in the columnar samples; the content of heavy metals in the columnar samples fluctuated serratedly with depth. The total amount of seven heavy metals reached the peak at 0.5 m and 2.0 m; all of them reached the class I standard of marine sediment quality in China; Cd was dominated by secondary phase, which was composed of the exchangeable and carbonate fractions (F1)、iron-manganese oxide states (F2) and organic matter and sulfide fractions (F3), The proportion of three fractions was similar; the mode of occurrence of Cu, Zn, Pb, Cr, As, Ni was residual state, and the trend of effective state of seven heavy metals was periodic and consistent. Take Ni as a reference, with three analytical methods,results showed that Cu, Zn, Pb, Cr, As and Ni are mainly natural deposition, and whether Cd is a threat to the environment still remains for further study. Through three analytical methods, we can observe the content and morphology changing by years of heavy metals by means of isotope dating, aiming to determine the historical records and influencing factors of heavy metal pollution. The pollution degree of heavy metals in surrounding waters near Ma'an Archipelago is much lower, and the ecological environment is totally well protected, and the environment is less affected by human factors, reflecting the results of local sediment background values.