We evaluate the bird-train collision risk associated with a recent high-speed railway project for the crested ibis (Nipponia nippon) and other local bird species in the Qinling Mountains, China. Using ground-walked line transect surveys, we surveyed the population abundance, distance to the railway bridge, and bridge-crossing behaviors of the birds in the study area. The results show that: (1) The crested ibis and the little egret (Egretta garzetta) were the two most abundant waterfowl species in the study area. The relative abundance index of these two species were about 43.33% and 42.75%, respectively; (2) 92.86% of the observed crested ibises were firstly detected within the range of 0 m to 25 m of the vicinity of the railway bridge; (3) The ratio between crossing over and under the railway bridge is about 7:3, which we found that crested ibises preferred flying over the bridge, but little egrets were more likely to cross the railway below the bridge. In the end, we recommend that, while the collision risk for the crested ibis could be low, protection structures, such as barrier poles or fences, should still be considered to avoid possible collisions of other co-habitants and promote conservation for multiple bird species in the area.