The deep sea, characterized by darkness, low temperatures, limited food availability, and extreme pressure, harbors a diverse array of life forms. Deep-sea fish, which have evolved unique adaptations to thrive in these harsh conditions, play a crucial role in marine ecosystems and biogeochemical cycles. This study investigated the trophic ecology and mercury (Hg) dynamics of eleven deep-sea fish species in the East China Sea (ECS) using stable isotope analysis (SIA) and total mercury (THg) concentration. Our findings revealed significant overlap in trophic niches among the examined species, with notable exceptions indicating instances of competition and resource partitioning. Coelorhynchus anatirostris exhibited a relatively broader trophic niche, suggesting a generalist feeding strategy, while Chlorophthalmus albatrossis and Neoscopelus microchir displayed more specialized niches. We identified four distinct trophic guilds based on δ13C and δ15N values, as well as THg concentrations, which underscore the complex interactions of niche differentiation and resource sharing within the deep-sea community. The incorporation of Hg as an additional bioindicator provided valuable insights into feeding strategies and trophic levels, highlighting its effectiveness in distinguishing ecological niches. Positive correlations between THg concentration and total length were observed in certain species, but not across all. At the community level, THg concentrations were closely associated with trophic level and habitat. Notably, THg concentrations in demersal fish were significantly lower than those in mesopelagic fish, likely attributable to the intricate distribution of THg within the ECS, suggesting the complexity of THg variation with depth. Our results demonstrate how vertical habitat partitioning and dietary preferences mediate competition and coexistence among deep-sea fish species in the ECS. These findings advance our understanding of deep-sea ecosystem trophic structure and function while providing insights for conservation and management strategies.