Bivalves are extensively employed as biomonitors of coastal pollution, but the comparability among different species and geographic environments needs to be further scrutinized. The present study conducted a meta-analysis of trace metals (Ag, Cd, Cr, Cu, Ni, Pb, Ti, and Zn) in the soft tissues of three groups of marine bivalves (oysters, mussels, and clams) collected from China and worldwide. By conducting cumulative frequency distribution analysis of metal distribution, we modeled the 5% cumulative values as the bio-baseline metal concentrations in these bivalves. We further modeled their potential baseline concentrations using a well-developed biokinetic model. The baseline concentrations of Cd, Cu, and Zn in the tissue-specific Environmental Quality Standards (EQSs) for China were 0.99, 34.5, and 340 μg/g dw in oysters, 0.38, 4.32, and 49.6 μg/g dw in mussels, and 0.35, 3.02, 51.4 μg/g dw in clams, respectively. Of the 8 metals examined in this study, the calculated baseline concentrations of Ag, Cr, Cd, Cu and Zn in the oysters were 3.7–48, 2.7–3.6, 2.6–2.8, 8.0–11.4, 6.6–6.8 times higher than those in the mussels and clams, and only Ti showed comparable baseline concentrations among the three bivalves (8.43–9.67 μg/g dw). These data strongly suggested the inter-group as well as inter-metal difference in the baseline metal concentrations in marine bivalves. Further, the potential baseline concentrations of Cd and Cu predicted by the biokinetic model were comparable to those modeled by the probability frequency distribution. Combined statistical frequency analysis and biokinetic modeling therefore provided an innovative method to establish the baseline metal concentrations in bivalves and the tissue-specific EQSs, which are now urgently needed for coastal management, biomonitoring, and geochemical records in the world.