Taking Futian Mangrove National Nature Reserve as the study area, sediments cores (0–50 cm) were sampled among three kinds of habitat, including fish pond, Avicennia marina forest and mudflat. The spatial distribution features of physicochemical properties and heavy metals in sediment cores were analyzed. The potential ecological risk index of heavy metals was calculated and analyzed. Analysis of physicochemical properties revealed that pH value followed the order: mudflat>Avicennia marina forest>fish pond; electrical conductivity, salinity, and total organic carbon (TOC) followed the order: Avicennia marina forest>mudflat>fish pond. The metal concentrations in sediments decreased in the following order: Zn (103.45–214.14 μg/g), Cu (70.92–133.50 μg/g), Pb (54.90–84.65 μg/g), Cd (6.57–7.25 μg/g). The concentrations of Zn, Cu and Pb followed the order: Avicennia marina forest>mudflat>fish pond and the concentrations of Cd followed the order: Avicennia marina forest≈mudflat>fish pond. The lowest level was located at fish pond (P<0.05). The concentrations of Zn and Cu were extremely different (P<0.05) among different vertical depths. Only the concentration of Cu was significantly affected by the interaction effect of sites and depths (P<0.05). Bivariate correlations results indicated that TOC had a significantly positive correlation with Pb in the fish pond (P<0.05), and the correlation of different kinds of heavy metals were complicated in Avicennia marina forest and mudflat. Different kinds of heavy metals had a significantly positive correlation in the fish pond (P<0.05), indicating that the source of 4 species of heavy metals might be same. In addition, the average contents of Cd, Cu, Zn, and Pb in all sediments of the Futian Mangrove Nature Reserve exceeded the first class of criteria GB 18668-2002．The single potential ecological risk of heavy metals followed the order: Cd>Cu>Pb>Zn and Avicennia marina forest>mudflat>fish pond. The integrated potential ecological risks at sampling sites reached high risk level completely, mainly due to Cd contamination, followed by Cu.