The organic matter in sediments can mineralize over time, which impacts the morphology of the heavy metals therein, which in turn affects the assessment of the risks posed by heavy metals. We used the sediments of Bohai Bay as the study object and analyzed the effects of different organic carbon mineralization levels on the concentrations of heavy metals (Cr, Pb, Cu, Zn, and Cd) using water extraction and potassium permanganate oxidation. The mean concentrations of Cd, Pb, Cu, and Zn in Bohai Bay were within the limits recommended by the World Health Organization. The proportions of the active and inert organic carbon fractions were 61.72% and 32.94%, respectively. Organic carbon mineralization most strongly impacted Cd and Pb levels, with releases accounting for 47.92% and 25.75%, respectively, of the oxidizable fractions. The release of all heavy metals, except for Cr, increased with increases in organic carbon mineralization, and heavy metals were released at a maximum rate of 12.94% when the organic carbon was highly mineralized, whereas Cr was released at a maximum of 0.023% during the first stage of organic carbon mineralization. In terms of spatial distribution, the concentration of mineralizable organic carbon in the sediments of the estuaries was substantially higher than that in other marine areas. Estuary sediments were more easily affected by organic carbon mineralization; therefore, the heavy metals in the oxidizable fraction of the estuarine region were more easily transformed into unstable heavy metal forms, posing high risk levels. Therefore, this study highlights the effects of organic carbon mineralization on heavy metal morphology and stability, when evaluating the ecological risk of heavy metals in marine sediments.