The concentration of trace elements (TEs) and their risk to narrow-ridged finless porpoises (Neophocaena asiaeorientalis) are still unclear. The present study determined the concentration of typical TEs in liver, kidney, and muscle tissues from porpoises in the East China Sea, assessed potential health risk of TEs to porpoises, and explored the relationship between TE concentration and metallothionein genes (MTs) polymorphism. It was found that Zn, Cu, Mn, Cd and Hg were highly accumulated in liver, and Cd was highly accumulated in kidney. The concentrations of Cr, As, Pb and Ni were very low in all three tissues. TE concentrations showed significant positive correlation with body length, and sexual variation. The levels of most TEs were higher in tissues of porpoises in Ningbo and Nantong than in Pingtan, which is likely related to the local environment pollution level. The risk assessment showed that porpoises from Nantong and Ningbo could face health risks due to Hg, As, Cd, Pb, and Cr exposure. Moreover, two polymorphic sites on the MT4 gene were found to be significantly associated with increased levels of Hg, Cd, Zn and Mn. Whether these two polymorphic sites are involved in expression of MTs, or other functional processes, needs further research.