Abstract: The Volume of Fluid (VOF) method was employed to track the water-air interface, and the fluid was described using the incompressible fluid continuity equation and motion equations. A three-dimensional numerical flume was established using nested grid technology, with turbulence modeled through the RNG k–ε model, while sediment transport was based on the Van Rijn method. Using the validated numerical flume model, this study investigates the local hydrodynamic and scouring behavior of pile foundations with pile cap structures under varying flow conditions. The distribution of flow fields around the pile, sediment transport, and local scour characteristics of the bed surface were analyzed. The results indicate that scour behavior is influenced by factors such as scouring duration, flow velocity, water level, flow angle, and pile spacing. At lower flow velocities, the interactions between individual piles in a pile group are minimal, and the sediment erosion and deposition patterns are similar to those of a single pile. However, at higher flow velocities, the upstream piles significantly shield the downstream piles, with vortex shedding from the upstream piles affecting the flow around the downstream piles, resulting in reduced flow velocities. This leads to the formation of a group scour pit, where the scours around individual piles coalesce, and elongated scour pits develop between the last row of piles, reaching the greatest scour depth.