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Abstract Structural inversion of rifted basins is generally associated with surface uplift and denudation of the sedimentary infill, reflecting the active contractional deformation in the crust. However, worldwide examples of inverted rifts show contrasting basin-scale subsidence and widespread sedimentation patterns during basin inversion. By conducting a series of three-dimensional coupled geodynamic and surface processes models, we investigated the dynamic controls on these subsidence anomalies during the successive stages of rifting and basin inversion, and we propose a new evolutionary model for this process. Our models show that the inherited thermo-rheological properties of the lithosphere influence the initial strain localization and subsequent migration of crustal deformation during inversion. The sense of the vertical movements (i.e., uplift or subsidence), however, is not directly linked to the underlying crustal stress patterns; rather, it reflects the balance among contraction-induced tectonic uplift, postrift thermal subsidence of the inherited lithosphere, and sediment redistribution. Based on the interplay among the competing differential vertical movements with different amplitudes and wavelengths, inversion of rifted basins may lead to the growth of intraplate orogens, or the contraction-driven localized uplift may be hindered by the thermal sag effects of the inherited shallow lithosphere-asthenosphere boundary, resulting in basin-scale subsidence. In such basins, dating the first erosional surfaces and other unconformities may not provide accurate timing for the onset of inversion.