This study utilizes three-dimensional simulations to investigate scour in combined wave–current flows around rectangular piles with various aspect ratios. The simulation model solves the Reynolds-averaged Navier–Stokes (RANS) equations using the k–ω turbulence model, and couples the Exner equation to compute bed elevation changes. The model also employs the level-set approach to realistically capture the free surface, and couples a hydrodynamic module with a morphological module to simulate the scour process. The morphological module employs a modified critical bed shear stress formula on a sloping bed and a sand-slide algorithm for erosion and deposition calculations in the sediment bed. To validate the numerical model, simulations are conducted in a truncated numerical wave tank with the Dirichlet boundary condition and active wave absorption method. After validation, the numerical model is used to investigate the effect of aspect ratio and the Keulegan–Carpenter (KC) number on scour depth in a combined wave–current environment. The study finds that the normalized scour depth is highest for a rectangular pile with an aspect ratio of 2:1 and lowest for an aspect ratio of 1:2. The maximum normalized scour depth (S/D) for aspect ratios of 2:1 are 0.151, 0.218, and 0.323 for KC numbers 3.9, 5.75, and 10, respectively, whereas the minimum normalized scour depth (S/D) for aspect ratios of 1:2 are 0.132, 0.172, and 0.279. Additionally, the research demonstrates that the normalized scour depth increases with an increase in the KC number for a fixed wave–current parameter (Ucw).@en