Abstract: Qinling lenok Brachymystax tsinlingensis, a threatened salmonid species endemic to the Qinling Mountain Range, is currently experiencing a population decline and holds the status of a second-class state-protected wild animal in China Red Data Book of Endangered Animals. Scientific and effective investigation and assessment of the population size of this species have been lacking for an extended period, along with systematic research on the distribution patterns of its larval fish and the environmental characteristics of its habitats. This study aims to elucidate the distribution patterns of larval B. tsinlingensis and the environmental drivers, thereby providing a research basis for early resource conservation efforts for the species. In this study, the trunk stream Puyu River and its tributary Mulashigou River in the Qinling Lenok National Nature Reserve, Longxian, Shaanxi Province, China, were selected as the study sites. 100 sample squares (2 m×2 m) were set up as detailed sampling habitats. The results showed that: (1) The number of larval B. tsinlingensis distributed in tributary was significantly higher than that in the trunk stream (P<0.05). (2) The population size of larval B. tsinlingensis showed an increasing and then decreasing trend with altitude. The optimal distribution altitudes in the trunk stream and tributary were 1460 and 1446 m, respectively. (3) Environmental drivers influencing larval B. tsinlingensis distribution varied between the trunk stream and tributary, with larval B. tsinlingensis abundance in trunk stream significantly negatively correlated (P<0.05) with flow velocity and green moss abundance, while positively correlated (P<0.05) with larval caddis worm abundance. In contrast, larval B. tsinlingensis abundance was significantly negatively correlated (P<0.05) with flow velocity and positively correlated (P<0.05) with tadpole and larval caddis worm abundance in the tributary. This study revealed the distribution patterns of larval B. tsinlingensis and the environmental characteristics of their habitats. Additionally, it constructed a heat map illustrating the relationships between various environmental drivers in larval B. tsinlingensis habitats. These findings will provide the necessary scientific basis for the investigation and monitoring of Qinling lenok populations, as well as for habitat suitability assessment, conservation, and ecological restoration for this species.