<p>Collaborative changes in the hydro-sediment regime and erosional base level are vital factors that influence the evolution of wandering rivers. In the wandering Xiaobeiganliu reach of the Middle Yellow River (MYR), the rapidly decreasing sediment discharge and lowering base level, i.e., the Tongguan elevation, have resulted in new features of thalweg migration in river morphology. In this work, on the basis of topographic measurements of the reach from 2003–2021, the thalweg migration distance and intensity were calculated at both the section scale and reach scale. The results revealed that the annual sediment discharge decreased by 72% from 1986–2002, and the reach exhibited sustained scouring from deposition, leading to the Tongguan elevation decreasing by 1.69 m compared with that in 2002. Accordingly, the distance and intensity of thalweg migration have been reduced to varying degrees in both section and reach scales. The maximum section-scale thalweg migration distance was reduced by 11%, whereas the average thalweg migration distance and intensity at the reach scale decreased by 14% and 43%, respectively. During this sustained scouring period, the fluvial erosion intensity at the reach scale increased as the sediment discharge decreased. However, because the base level remained high, riverbed undercutting was deeply limited, which exacerbated lateral erosion of the bank and floodplain, enhancing thalweg migration. Flow-sediment regulation and training can be coupled to increase undercutting efficiency in the main channel and to protect banks from lateral erosion in river reach management.</p>