The tissue distribution (liver, kidney, heart, lung, and muscle), source, and trophic transfer of 15 polycyclic aromatic hydrocarbons (PAHs) were studied on 14 stranded East Asian finless porpoises (Neophocaena asiaeorientalis sunameri), 14 spotted seals (Phoca largha), and 9 stranded minke whales (Balaenoptera acutorostrata) from Yellow Sea and Liaodong Bay. The PAHs levels ranged from below the limit of detection to 459.22 ng g−1 dry weight in the tissues of the three marine mammals, and light molecular weight PAHs were the primary pollutants. Although the PAHs levels were relatively higher in internal organs of the three marine mammals, generally no tissue-specific distribution of the PAHs congeners was found, either for gender-specific distribution of PAHs in the East Asian finless porpoises. However, species specific PAHs concentration distribution were obtained. The PAHs were mainly originated from petroleum and biomass combustion in the East Asian finless porpoises, while those for the spotted seals and minke whales were complex. Trophic level associated biomagnification was found for phenanthrene, fluoranthene, and pyrene in the minke whale. Benzo(b)fluoranthene exhibited a significant biodilution with increasing trophic levels in the spotted seals, but the total concentration of the PAHs showed a significant biomagnification with increasing trophic levels. Trophic level-associated biomagnification of acenaphthene, phenanthrene, anthracene, and ∑PAHs were found in the East Asian finless porpoise, while pyrene exhibited obvious biodilution with increasing trophic levels. Our current study filled knowledge gaps on tissue distribution and trophic transfer of the PAHs in the investigated three marine mammals.