The Tianshan orogenic belt is an intracontinental orogenic belt that has been revived and uplifted since the Cenozoic. Thus, understanding and appreciating the deep structure and basin-mountain coupling relationships in Tianshan orogenic belt are particularly important due to the strong seismic activity. The phase-velocity dispersion curves of the 6-52 s Rayleigh wave were obtained in this paper using the cross-correlation method of ambient noise based on the ambient noise data from 85 stations in the Tianshan orogenic belt and adjacent areas (40°-49°N, 79°-93°E) during 2017-2019. The direct inversion method of surface waves based on ray tracing was employed to investigate the 3D crustal S-wave velocity structure and basin-mountain coupling relationship in the middle Tianshan Mountains. Results show that the S-wave velocity distribution in the shallow crust is related to the thickness of sedimentary layers in the tectonic unit, demonstrating low velocity in the northern margin of Tarim Basin and the southern margin of Junggar Basin and high velocity in the Tianshan orogenic belt. Low-velocity bodies wrapped by high-velocity anomalies below the Tianshan orogenic belt are found in the middle and lower crusts; the Tianshan orogenic belt shows relatively low velocities near the Moho surface. The crustal thicknesses of the southern margin of Junggar Basin and the Tianshan orogenic belt are in the range of 45-50 and 50-62 km, respectively. Between 82°-86.5°E, Tarim and Junggar Basins are subducted bidirectionally below Tianshan Mountains; between 86.5°-88°E, the Junggar Basin is subducted southward to Tianshan Mountains. From west to east, different basin-mountain coupling relationships reveal the difference in tectonic movement in different regions of the middle Tianshan Mountains since the Cenozoic, thus providing a reference for further exploration of orogenic dynamical processes.