Herein, we investigated the trophic transfer of mercury (Hg) through food chains in different habitats (namely aquatic, riparian, and terrestrial) through bulk stable isotope analysis of nitrogen (δ¹⁵N_bulk) and compound-specific isotope analysis of nitrogen in amino acids (δ¹⁵N_AA) using bird feathers and their potential food sources from a Hg-contaminated site in southwest China. Results showed similar δ¹⁵N_phe for water birds (4.7 ± 2.6 ‰) and aquatic food sources (5.2 ± 2.1 ‰) and for land-based food sources (10.1 ± 0.4 ‰) and terrestrial birds (11.6 ± 3.0 ‰), verifying δ¹⁵N_phe as a potential discriminant indicator for different food sources. The trophic positions (TPs) of most organisms based on δ¹⁵N_bulk (TP_bulk) tended to overestimate compared with those based on δ¹⁵N_AA (TP_AA), especially for predators (such as kingfisher: ΔTP = 1.3). Additionally, significant differences were observed in the aquatic, riparian, and terrestrial food webs between trophic magnification slope (TMS)_bulk and TMS_AA (p < 0.05). The trophic magnification factor (TMF)_AA-multiple based on multiple-AAs in three food webs were higher than the TMF_AA and TMF_bulk, probably because of the greater variation of δ¹⁵N_baseline, complex food sources or the notably different in individual organisms. Altogether, our results improve the understanding of Hg trophic transfer in aquatic, riparian, and terrestrial food webs.