Abstract: Since the Cenozoic, the far effect of the collision between the Indian–Eurasian continents has resulted in the continuous northward expansion of the northeastern margin of the Qinghai–Tibetan Plateau. The North Qilian–Beishan block, located at the northern margin of the Tibetan Plateau and the southern margin of the Central Asian orogenic belt, is a key area to document the expansion frontier. In this paper, we utilize the tomography of the seismic refraction wave Pg traveltime data from the wide-angle reflection & refraction profile to obtain the 350 km-long basement velocity structure. The result shows that the sediment thickness varies significantly along the profile, ranging from 6 to 8 km with the deepest in the southern part of the Beishan block. Furthermore, a number of high-velocity bodies were found in the sedimentary cover. Combined with other geological and geophysical data, we suggest that the southern Beishan margin fault (SBMF) is a regional large-scale strike-slip fault zone, and the velocity structure of the North Qilian–Huahai Basin south of the SBMF is mainly normal with a gradient, and the northern North Qilian margin fault has been extended into the Jiuquan Basin. Whereas the basement velocity structure of the Beishan block north of the SBMF shows a multilayered velocity overlap, which indicates that the sedimentary cover in this area has developed multiple north-dipping thrust faults, and fold-thrust nappe structures, which accommodated the upper crustal shortening in the northern part of the Beishan Mountains.