Bird collisions with high-speed transport modes is a vital topic on vehicle safety and wildlife protection, especially when high-speed trains, with an average speed of 250km/h, have to run across the habitat of an endangered bird species. This paper evaluates the bird-train collision risk associated with a recent high-speed railway project in Qinling Mountains, China, for the crested ibis (Nipponia nippon) and other local bird species. Using line transect surveys and walking monitoring techniques, we surveyed the population abundance, spatial-temporal distributions, and bridge-crossing behaviors of the birds in the study area. The results show that: (1) The crested ibis and the egret were the two most abundant waterfowl species in the study area. The RAI of these two species were about 43.69% and 42.91%, respectively; (2) Crested ibises overall habitat closer to the railway bridge. 91.63% of them were firstly detected within the range of 0m to 25m of the vicinity of the bridge; (3) the ratio between crossing over and under the railway bridge was about 7:3. Crested ibises were found to prefer to fly over the railway bridge (89.29% of the total crossing activities observed for this species). Egrets were more likely to cross the railway below the bridge, and they accounted for 60.27% of the total observations of crossing under the bridge. We recommend that, while the collision risk of crested ibises could be low, barrier-like structures, such as fences, should still be considered to promote the conservation of multiple bird species in the area. This paper provides a practical case for railway ecology studies in China. To our best knowledge, this is the first high-speed railway project that takes protecting crested ibises as one of the top priorities, and exemplifies the recent nationwide initiative towards the construction of eco-civilization in the country.