In order to remove heavy metals, different concentrations of ethylene diamine tetraacetic acid disodium (EDTA-Na2) and fytic acid were separately added during the extraction of fucoidans from brown seaseeds, and the prepared products were determined by inductively coupled plasma-mass spectrometry (ICP-MS) and hydride generation atomic fluorescence spectroscopy (HGAFS) for the contents of metal elements (such as Mg, Ca, Fe, Mn, Cu, Zn, Ag, Cd, Ba, Pb, As and Hg). Adding 1.0 ×10-2 mol/L EDTA-Na2 could efficiently reduce the contents of Mg, Ca, Mn, Zn, As, Ag, Cd and Pb in the prepared fucoidans, but had no effect on Hg, Fe, Cu and Ba. However, only Ag, Cd and Zn exhibited lower contents due to the addition of 0.10 mol/L fytic acid. The simultaneous binding of As and Hg to fucoidans was conducted in order to evaluate the efficiency of removing heave metal element by acidic treatment followed by ultrafiltration. As a result, no As was detected in the ultrafiltration retenate, while Hg was kept bound with fucoidans after acidic treatment and could not be removed. Thus, adding an appreciate concentration of EDTA-Na2 during extraction and acidic treatment followed by ultrafiltration during purification can obviously reduce the contents of heavy metal elements in the prepared fucoidans. This study provides a good strategy for preparing high-quality fucoidans.