The reconstruction of heavy metals record in coastal sediment core can improve the acknowledgement on the history of their usage/emissions in the coastal areas and the related river basins. In recent years,more and more reports have indicated the gradually increased emissions of various heavy metals into the shelf seas in China. However, the emission and accumulation history of multiple heavy metals have been less referred. In the present work, the contents of heavy metals (such as V, Cr, Zn, Ni, Cu, Co, As, Pb, Hg and Cd) from two sedimentary cores of DH33 and KP04 in the inner shelf of the East China Sea have been measured for studying their history records and then evaluating their ecological risks in the past. The Pearson correlations between these heavy metals have been used for evaluating their accumulation process and the influencing factors. Also the ecological risks have been performed by using potential ecological risk index during the last 100 years. Our results showed that the contents of V, Cr, Zn, Ni, Cu, Co, As, Pb, Hg and Cd in DH33 were 6669±582, 4872±369, 5688±372, 2682±134, 780±076, 1265±063, 399±025, 1277±091, 0042±0008 and 0069±0005 mg/kg respectively, while they were 6658±160, 4937±345, 8562±636, 2990±160, 1171±076, 1345±103, 767±102, 1904±110, 0044±0004 and 0007±0004 mg/kg respectively in KP04. By comparing with the interannual runoff variation of the Yangtze River, it was found that the accumulative process was strongly correlated with the annual runoff of the Yangtze River. The contents of these heavy metals except Cd in core KP04, which is farther away from the Yangtze Delta and the coastline, were higher than those in DH33. The results were in conflict with the geological locations and the “granularity law”. This could be attributed to the different accumulation process or controlling factors in the two sea regions. The contents of heavy metals in core DH33 were mainly controlled by the Yangtze River runoff, with higher accumulations in larger runoff years. In core KP04, their accumulations of these heavy metals were controlled by the provenance supply and the sedimentation rate, with Taiwan Warm Current as another important provenance source. Significant correlations between V, Cr and Ni have been observed, suggested their possible origin and accumulation mechanism. The poor correlations of As, Hg and Cd with other metals suggested their different origins and accumulation process in marine settings. The evaluation on the ecological risk showed that there was only “moderately polluted” by Hg, Cd and As in KP04 and it happened in 1990s and 1930s. Comparing with the deltas and coastal areas, the overall ecological risks of heavy metals were at lower levels in the inner shelf. The potential risks of Hg, Cd and As still needed to be concerned because of their bioaccumulations along the food chain