The Helan Mountains and Yinchuan Basin (HM-YB) are located at the northern end of the North-South tectonic belt, and form an intraplate tectonic deformation zone in the western margin of the North China Craton (NCC). The HM-YB has a complicated history of formation and evolution, and is tectonically active at the present day. It has played a dominant role in the complex geological structure and modern earthquake activities of the region. A 135-km-long deep seismic reflection profile across the HM-YB was acquired in early 2014, which provides detailed information of the lithospheric structure and faulting characteristics from near-surface to various depths in the region. The results show that the Moho gradually deepens from east to west in the depth range of 40–48 km along the profile. Significant differences are present in the crustal structure of different tectonic units, including in the distribution of seismic velocities, depths of intra-crustal discontinuities and undulation pattern of the Moho. The deep seismic reflection profile further reveals distinct structural characteristics on the opposite sides of the Helan Mountains. To the east, The Yellow River fault, the eastern piedmont fault of the Helan Mountains, as well as multiple buried faults within the Yinchuan Basin are all normal faults and still active since the Quaternary. These faults have controlled the Cenozoic sedimentation of the basin, and display a “negative-flower” structure in the profile. To the west, the Bayanhaote fault and the western piedmont fault of the Helan Mountains are east-dipping thrust faults, which caused folding, thrusting, and structural deformation in the Mesozoic stratum of the Helan Mountains uplift zone. A deep-penetrating fault is identified in the western side of the Yinchuan Basin. It has a steep inclination cutting through the middle-lower crust and the Moho, and may be connected to the two groups of faults in the upper crust. This set of deep and shallow fault system consists of both strike-slip, thrust, and normal faults formed over different eras, and provides the key tectonic conditions for the basin-mountains coupling, crustal deformation and crust-mantle interactions in the region. The other important phenomenon revealed from the results of deep seismic reflection profiling is the presence of a strong upper mantle reflection (UMR) at a depth of 82–92 km beneath the HM-YB, indicating the existence of a rapid velocity variation or a velocity discontinuity in that depth range. This is possibly a sign of vertical structural inhomogeneity in the upper mantle of the region. The seismic results presented here provide new clues and observational bases for further study of the deep structure, structural differences among various blocks and the tectonic relationship between deep and shallow processes in the western NCC.