Using the Ecopath approach and a network analysis, a mass-balance trophic model was constructed to analyze the structure and energy flows of a high-altitude subtropical headwater stream, Chichiawan Stream, the only habitat of the Critically Endangered Formosan landlocked salmon Oncorhynchus formosanus. Natural abundances of carbon and nitrogen isotopes (δ 13 C and δ 15 N) were used as a complementary method to stomach content analysis to trace food sources of consumers in the stream. Riparian C 3 plants were the major food source of dominant gatherer and filterer aquatic insects, while diatoms were the major food source of scraper aquatic insects. Lindeman trophic analysis indicated that the flows of detritivory and herbivory were quantitatively equally important as food sources for consumers in the stream, suggesting a close terrestrial−aquatic linkage. The trophic model of Chichiawan Stream comprised 13 compartments and 4 integer trophic levels with the highest trophic level of 3.12 for birds. The pedigree index for the trophic model was 0.71, indicating a high-quality model. The mixed trophic impacts indicated that the biomass of Formosan salmon was unlikely constrained by food sources or predation pressure by birds. In a comparative analysis with other trophic models of temperate mountain streams, the total consumer biomass and mean trophic transfer efficiency were relatively low in this subtropical mountain stream, which is characterized by high precipitation, steep channels, rapid current velocity, and changing flow regime. To conserve the Formosan salmon, the first priorities are agricultural runoff control and maintaining a well-vegetated riparian zone.