Abstract: The Qilian Orogenic Belt, located at the northeastern margin of the Tibetan Plateau with the Central Qilian Block at its core, plays a significant role in regional tectonic evolution. To reveal the crustal velocity structure of the Qilian Orogenic Belt and investigate the relationship between velocity structure and seismic activity, this study utilized P-wave and S-wave arrival time data recorded by seismic networks in Gansu, Qinghai, and other regions under the China Earthquake Networks Center. A double-difference tomography method was applied to relocate 6,617 seismic events in the study area, and 3D P-wave/S-wave velocity structures as well as velocity ratio distributions were obtained. The double-difference tomography produced several interesting results: (1) The Central-Northern Qilian Fault Zone exhibits distinct segmentation in activity along its eastern and western sectors. The eastern segment is dominated by shallow-seated faulting (0-10 km), whereas the western segment features deeper-seated tectonic activity (15-25 km). This indicates more pronounced upper crustal thickening in the western sector of the Qilian orogenic belt. Large earthquakes are concentrated in high-velocity anomaly regions of the upper-middle crust, suggesting that brittle crust is more prone to fault rupture. (2) Both velocity structures and velocity ratio distributions show a vertical transition from high to low values, indicating that the upper-middle crust of the Qilian Orogenic Belt is more rigid, whereas the middle-lower crust may include dehydration reactions of hydrous minerals. (3) There is a significant interface separation between the Central Qilian Block and the North Qilian Orogenic Belt in the upper–middle crust, which corresponds well with the south-deep and north-shallow distribution characteristics of sedimentary rock layer thickness in the Qilian Orogenic Belt.