Sustainable management of sediment-laden rivers is essential for balancing flood control, ecological protection, and socioeconomic development. The Upper Yellow River, supporting 160 million people, faces escalating challenges in maintaining channel stability under intensified water–sediment imbalances. This study investigates the Sipaikou reach in Ningxia—a representative wandering channel with multiple mid-channel shoals—through integrated UAV-USV-GNSS RTK field measurements and hydrodynamic and sediment transport modeling. Field measurements reveal that mid-channel shoal morphology coupled with bend circulation governs flow division patterns, with discharge ratios of 44.16% and 86.31% at the primary and secondary shoals, respectively. Gaussian kernel density estimation demonstrates velocity distributions evolving from right-skewed to left-skewed around shoals, while spur dike regions display strong left skewness with concentrated main flow. Numerical simulations under six discharge scenarios indicate: (1) Head loss exhibits diminishing marginal effects at the primary shoal, an inflection point at a critical discharge at the secondary shoal, and superlinear growth in the spur dike region. (2) The normal-flow period represents the critical threshold for erosion–deposition regime transition. (3) Spur dike series achieve bank protection through main flow constriction and inter-dike low-velocity zone creation. These findings provide scientific foundations for sustainable flood risk management and ecological restoration in wandering rivers. The integrated measurement–simulation framework offers a transferable methodology for adaptive river management under changing hydrological conditions.