In this paper, three sampling sites, namely a non-invaded Cyperus malaccensis wetland (A), a Spartina alterniflora-invaded patch edge (B) and a Spartina alterniflora-invaded wetland (C) were selected to examine the effects of Spartina alterniflora invasion on heavy metal accumulation in estuarine wetland sediments. Sediment Cobalt (Co), Nickel (Ni), Copper (Cu) and Arsenic (As) at 10 different depths were analyzed and then evaluated using geo-accumulation indexes and potential ecological risks evaluation methodology. The results suggested that: (1) Co, Ni, Cu and As in sediments increased with the invasive time of Spartina alterniflora (i.e. C>B>A), and the retention of Co, Ni, Cu and As increased by 26.31%, 19.66%, 50.79% and 16.93%, respectively. (2) According to the geo-accumulation indexes, Co, Ni and Cu in the research area were slightly polluted and As experienced a transitional period from strongly polluted to extremely polluted. (3) The potential ecological risks of Co, Ni and Cu were low, however As at sites A and B was in high potential ecological risk and that at site C was in very high risk. The results of both methods showed that Spartina alterniflora invasion increased heavy metal pollution and potential ecological risks. And more attention should be given to the As pollution in the research area. Finally, the heavy metals in sediments were significantly correlated with total carbon, total nitrogen, C/N, bulk density and aboveground biomass, which indicated that the accumulation of heavy metals might be related to the developed biomass aboveground and the dense root structure underground of Spartina alterniflora.