Sediment samples were collected in five marshes (C1, Phragmites australis marsh; C2, P. australis and Cyperus malaccensis marsh; C3, C. malaccensis marsh; C4, Spartina alterniflora marsh; and C5, Cyperus compressus marsh) respectively along two typical transects (T1 and T2) extending from the vegetated marsh to the mudflat in a typical subtropical estuary (Min River) of China in July 2015 to investigate the spatial variation and toxicity of heavy metals (Pb, Cr, Cu, Zn, and Ni) in intertidal zone. Results showed that the concentrations of heavy metal in surface sediments of the two transects were in the order of Zn > Cr > Pb > Cu > Ni and slightly decreased from the land to the sea except for Pb and Zn. The levels of the five metals at C5 marsh were generally the lowest, while those of Pb, Cr, and Zn at C2 marsh were the highest. The vertical variations of Pb, Cr, and Zn concentrations in profiles differed among marshes or transects, and in most cases, there was no evidence of sediment organic matter (SOM) contributing to the sorption of significant amount of metals in sediments along the two transects, while grain composition was a primary factor controlling the spatial variations of metals. Both the vertical distributions of Cu and Ni levels among marshes or transects showed little fluctuation, which could be better explained by the effects of sulfur on the solubility and mobility of the two metals in profiles. Heavy metal levels in sediments of the Min River estuary were much higher compared with most estuaries in Asia, Europe, Africa, and South America. The sediments in intertidal zone of the Min River estuary were moderately polluted by the five metals, and particularly, Ni was identified as heavy metal of primary concern. Both Ni and Pb in sediments of the intertidal zone showed high potential toxicity and high contributions to the sum of the toxic units (Sigma TUs). In future, the metal pollutions in intertidal zone of the Min River estuary might be more serious, and in the next step, there will be long-term potential consequences for endangered animals or migrant birds if measures are not taken to rehabilitate the sediments resulting from metal pollutions.