Sediment flushing through bottom tunnels has been widely applied in engineering practice to alleviate reservoir sedimentation. However, there is limited understanding of whether flushing can be accomplished once the tunnel intake is covered by deposited sediment. Here, a three-dimensional model is used to resolve the hydro-sediment-morphodynamic processes and reveal the physical mechanism for the occurrence of reservoir sediment flushing through an initially covered bottom tunnel. The results demonstrate that the reservoir water level and initial cover layer thickness have a significant impact on the pressure difference between tunnel inlet and outlet and the resistance of tunnel walls, determining the momentum of the water-sediment mixture. If water level is low or cover layer is thick, the pressure is not sufficient to overcome the resistance. The momentum tends to zero, and tunnel blockage occurs. If water level is high or cover layer thickness is small, the scour hole depth will exceed the cover layer thickness and the sediment concentration in tunnel decreases. The resistance is reduced significantly, and sediment flushing is accomplished. The present work facilitates enhanced understanding of sediment flushing, thereby informing reservoir engineers and managers of potential approaches to benefit maximization and sustainable sediment management.