Heavy metals are major pollutants that pose threats to wetland environments. In the present study, surface sediments from wetlands vegetated by invasive species Spartina alterniflora in the Yellow River Delta were collected and determined for the mass fractions of Co, Ni, As, Cd and Pb. Results showed mass fractions of Co, Ni, As, Cd and Pb in the sediments of the S. alterniflora communities ranged from 8.5 to 16.0, 13.9–27.9, 3.2–13.8, 0.08–0.24, and 17.6–37.5 mg/kg dw, respectively, generally presenting an order of Pb > Ni > Co > As > Cd. The levels of heavy metals in sediments in the S. alterniflora communities were higher than those in the wetland vegetated by the native plant species Suaeda heteroptera. Correlations among metal elements were highly significant, suggesting that they might have the same sources. Clay and TOC were important factors affecting the spatial distribution of metals. The I_geo values of the investigated elements in the sediments were frequently lower than 0, revealing the slight pollution status of these metals. Relatively slight values of E_rⁱ and RI suggested that the potential ecological risks caused by the 5 metals were low. Our findings could provide a better understanding of the correlation between metal pollution and bio-invasion in wetland ecosystems.