An investigation of stranded dolphins from Xiamen Bay revealed that the Indo-Pacific humpback dolphin (Sousa chinensis) accumulates a variety of heavy metals (HMs) at concentrations that may pose a risk to their health. Foodborne ingestion is considered the major exposure route of marine mammals to environmental contaminants. The health risks of pollutant exposure are of increasing concern in marine mammals due to their large daily intake of food. However, prey fish trophic level and biomagnification trends have not been assessed, thus preventing a comprehensive analysis of HM pollution in food webs. Herein, we assessed the potential risk of HMs to S. chinensis by determining the concentrations of 11 HMs in 10 fish species (180 samples) representing the major prey species of dolphins in the waters of Xiamen Bay. The results of the study showed that zinc (Zn) and arsenic (As) were the most abundant metals in all prey fish, with Zn ranging from 3,812 ng/g ww in Mugil sp. to 7,939 ng/g in Coilia sp., and As ranging from 983 ng/g ww in Setipinna taty to 8,812 ng/g in Cynoglossus sp. The trophic levels of the prey fish were relatively high (from 4 to 5), and methylmercury (MeHg), Zn, cadmium (Cd), and chronium (Cr) exhibited biomagnification, indicating that S. chinensis has a relatively high potential to accumulate HMs. Thus, the risk assessment results indicated that As, selenium (Se), and MeHg may pose a threat to S. chinensis. The method established in this study will facilitate the monitoring of HM-associated health hazards in Indo-Pacific humpback dolphins.