Laser-based direct energy deposition (DED-LB/M) has been a promising option for the surface repair of structural aluminum alloys due to the advantages it offers, including a small heat-affected zone, high forming accuracy, and adjustable deposition materials. However, the unequal powder particle size during powder-based DED-LB/M can cause unstable flow and an uneven material flow rate per unit of time, resulting in defects such as pores, uneven deposition layers, and cracks. This paper presents a multiscale, multiphysics numerical model to investigate the underlying mechanism during the powder-based DED-LB/M surface repair process. First, the worn surfaces of aluminum alloy components with different flaw shapes and sizes were characterized and modeled. The fluid flow of the molten pool during material deposition on the worn surfaces was then investigated using a model that coupled the mesoscale discrete element method (DEM) and the finite volume method (FVM). The effect of flaw size and powder supply quantity on the evolution of the molten pool temperature, morphology, and dynamics was evaluated. The rapid heat transfer and variation in thermal stress during the multilayer DED-LB/M process were further illustrated using a macroscale thermomechanical model. The maximum stress was observed and compared with the yield stress of the adopted material, and no relative sliding was observed between deposited layers and substrate components.