Heavy metals in sediments from the tidal flats of northern Nantong are investigated for the first time. Twelve sediment cores were analyzed to learn the vertical profiles of heavy metals. Averagely, the sediment cores contain 67.77 mg/kg of Cr, 20.13 mg/kg of Cu, 61.95 mg/kg of Zn, 0.13 mg/kg of Cd, 16.49 mg/kg of Pb, 7.36 mg/kg of As, and 0.005 mg/kg of Hg. To assess the contamination levels of heavy metals, geo-accumulation index (Igeo) and enrichment factor (EF) values were calculated. The Igeo values of heavy metals range from −6.721 to 0.957, showing that most sediments are in uncontaminated condition and a few are moderately contaminated by heavy metals. EF values of most samples are smaller than 1.5, which indicates that most heavy metals in the samples are from natural weathering processes. Also, Pearson correlation coefficients and principal component analysis is applied to find out the sources of the heavy metals. The correlation further indicates that Pb, As, and Hg are likely from natural weathering processes while Cu, Cr, and Zn have both natural and a small portion of anthropogenic sources. Additionally, anthropogenic sources such as vehicles and agricultural irrigations mainly contribute to the slight Cd contamination in Haimen tidal flats.