The greater amberjack (Seriola dumerili) holds significant commercially and ecologically important large pelagic marine species in Taiwanese waters. The aim of this study was investigates its stomach contents and stable isotope signatures (δ13C and δ15N) were used to explore the trophic ecology and to detect the dietary variations by length, sex, and season and their associations with marine environmental characteristics. Utilizing a generalized additive model, we elucidate how marine environmental variables influence greater amberjack feeding habitats. Our findings revealed that the mixed layer depth and sea surface temperature explained the highest influence in the greater amberjack feeding ground. To reveal the trophic ecology of the greater amberjack and their ecosystem trophic dynamics, we used an innovative approach combining stomach content analysis (SCA) and stable isotope analysis (SIA) of carbon and nitrogen (δ13C and δ15N) coupled with Bayesian mixing model analysis. By contrast, some of the results in SIA were different from the most important food items identified in SCA; in general, they prefer to consume pelagic prey species. The Bayesian mixing models indicated that the target predator species diet structure was dominated by Trichiuridae and Leiognathidae prey species, as indicated by the highest δ15N values. The relationships of the greater amberjack weight and length were not significant with δ13C values (p > 0.05) but were significant (p < 0.001) with δ15N values. The relationships between trophic positions (TPs) in terms of length, sex, and season suggested an ontogenetic shift, with varied TP values between 4.01 and 5.18, indicating that the greater amberjack is the top-level predator species in the pelagic marine ecosystem. These findings can guide ecosystem-based adaptive fishery management and conservation because the local prey species depletion and variations in marine environmental conditions may affect greater amberjack fisheries in Taiwanese waters.