The distribution of heavy metals in tidal flat sediment is of great significance on the estuary environment. This study aims to find the heavy metal distribution mechanism at different parts of the tidal flat on the Yangtze Estuary, China. Eleven sediment cores were collected at the high, middle and low tidal flats of eastern Chongming Island in four seasons -spring, summer, autumn and winter. The contents of elements Al, Cu, Cr, Fe, Mn, Pb, Rb, S, Si, Sr, Zn, Zr and humic acid in the sediment were analyzed. Pearson correlation analysis and principle component analysis (PCA) were used to analyze the main factors for heavy metal distribution in the tidal flat. The results showed that the redox and pH conditions in the sedimentation environment, grain size and humic acid had a significant effect on the distribution of heavy metals in the sediment of the tidal flat. The leading factors for heavy metal distribution and migration in the sediments are different at different parts of the tidal flat. The main factors for heavy metal distribution in the sediment of the low tidal flat are the source of sediment and the hydrodynamic force, while in the middle and high tidal flats, the effect of humic acid increases. The heavy metal distribution in the sediments of the middle tidal flat is mainly affected by the redox and pH condition of the sedimentation environment and humic acid, while in the high tidal flat, humic acid is the main controlling factor for heavy metal distribution in the sediment.