Understanding thermal and structural evolution of sedimentary basin is a key to assessing the hydrocarbon prospect. In the common approach to reconstruction of this evolution, a priori knowledge of thinning factors and paleobathymetry is required (while necessary data is commonly not available), sub-basin crust and mantle lithosphere evolution is omitted, and information about basal heat flow (it is usually getting from published heat flow maps, while this data is highly unreliable) is used as a boundary condition. Automatic correction of the prescribed heat flow is performed to get a good matching of modeling results with measured present-day temperature and maturity indicators. As a result, the approach gives multiple solutions and leads to fluctuations in temperature and maturity without proper physical/geological justification. There is an alternative approach to thermal reconstruction, resolving simultaneously for lithosphere and sedimentary basin processes. It involves an inverse algorithm, which iteratively updates crustal- and mantle-thinning factors and paleowater depth until the input stratigraphy is fitted to desired accuracy. The potential of this approach is demonstrated through comprehensive study of a transect across the West Siberian basin. Different geological scenario was considered, parametric study on key parameters was done, and the thermal blanketing effect of sediments was demonstrated.