There has been increasing concern about trace element accumulation in finless porpoises over the past decades, while the long-term variation of its concentration has been little known. Since most soft tissues of porpoises in the past were not preserved until now, the bone tissue is the only ideal material available. Here, 27 East Asian finless porpoise bone samples collected from Nantong, the East China Sea during two periods (1984–1992 and 2009) were used to explore the temporal variation of nine typical elements’ concentration (Fe, Mn, Cu, Ni, Hg, Cr, Pb, As, and Cd, dry weight). An upward trend for total trace element accumulation from 329.04 mg/kg in 1984–1992 to 1535.81 mg/kg in 2009 was found; this could have resulted from the increasing industrial development in the Nantong region. The Mn, Fe, and As levels increased significantly while the concentrations of Cd, Cu, and Pb significantly decreased. Generally, our results suggested that most trace elements posed low threats to East Asian finless porpoises’ health during both periods, while elements Mn (2009), Ni (both periods), Fe (2009), and As (2009) posed a potentially higher health risk to porpoises. Thus, the trace element levels warrant concern and continuous monitoring.