Abstract Mangrove wetlands are under increasing pollution pressure from human activities due to rapid industrialization and urbanization of coastal regions. Many pollutants such as heavy metals may be accumulated via food chains to hazardous levels which will thus bring potential health issues to humans. In the present study, three species of crabs (Sesarma dehaani, Sesarma plicata, Macrophthalmus japonicus) and associated sediments from three mangrove habitats with different vegetation were collected from the mangrove wetlands in Qi'ao Island, South China to investigate the levels, bioaccumulation and dietary exposure of heavy metals including copper (Cu), zinc (Zn), manganese (Mn), cadmium (Cd) and chromium (Cr). Metal concentrations in sediment samples were 65–91, 212–247, 506–1256, 0.6–1.3, and 8.8–14 mg/kg dry weight for Cu, Zn, Mn, Cd and Cr, respectively. The spatial heterogeneity of these metals in mangrove sediments was observed with a descendant order of metal concentrations as Mn > Zn > Cu > Cr > Cd at each site. Species-specific and tissue-specific accumulation of metals was also found in mangrove crabs, both in the degree of accumulation of particulate metals and the tissues in which they were most abundant. All biota-sediment accumulation factors (BSAF) values >1 for Cd in each crab species suggested that the native mangrove crabs tended to be good tools for the monitoring of Cd pollution in mangrove forests. Results of the estimated daily intake (EDI) and target hazard quotient (THQ) suggested that consumption of the mangrove crabs in Qi'ao Island might subject local residents to potential health risks as far as the metals are concerned.