The Linhe Depression is the largest tectonic unit in the Hetao Basin. The recently discovered commercial oil flow in the structural trap of wells JH2X and S5 has proved that the Meso-Cenozoic strata in the Linhe Depression have great exploration potential. Research on the kinematic model for the Mesozoic–Cenozoic Linhe Depression is important for analysing the geological conditions of hydrocarbon accumulation. In this study, field observations, seismic interpretation and scaled analogue modelling are performed. The results prove that the Linhe Depression experienced different stages of tectonic evolution, such as compressional depression (K1l), conversion from contraction to uniform subsidence (K1g), extensional rifting (E2–N2) and strike-slip deformation (Q), during the Mesozoic–Cenozoic eras. The kinematic model of negative inverted basins was first established with the early differential compression superimposed by the late extension. The seismic interpretation and analogue modelling results show that Jilantai Sag in the southern part of the Linhe Depression was subjected to compression from the Bayanwulashan fold–thrust belt on the NW side and the Helanshan fold–thrust belt on the SE side during Early Cretaceous time. Meanwhile, the Hanghou Sag in the northern part of the Linhe Depression was only compressed by the Langshan fold–thrust belt from the NW direction. The rifted structure generated by the extension from the SE direction during the Cenozoic Era resulted in the negative inversion of the pre-existing thrusts in different patterns. The intensity of negative inversion is controlled by several key factors, such as dip angle and the patterns of thrust faults, along with different basement textures. The morphological changes in the forebulge zone developed during Early Cretaceous time are responsible for the development of the segmented Central fault zones in the Hanghou Sag.