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Previous studies have suggested that irregular echinoids exhibit higher survival rates than regular echinoids following mass extinctions. This study focuses on the irregular echinoid Claviaster libycus, investigating its flow field and scour behavior under extreme water flow conditions through numerical simulations and experiments. The numerical model Splash3D used in this study was modified from the open-source code Truchas developed by the US National Laboratory. Splash3D solves the three-dimensional incompressible Navier–Stokes equations. The fluid volume method describes the water surface kinematics and sand surface kinematics. Since C. libycusis semi-submerged in the sand, a discontinuous bi-viscosity model describes the rheological behavior of the bed material. The research findings indicate that when the gonopore of C. libycusfaces downstream, there is no evident horseshoe vortex flow, which contributes to reducing the occurrence of localized scour. This also validates the hypothesis of this study: the transition of echinoids from pentaradial symmetry to bilateral symmetry assists in stabilizing bottom sediments and reducing localized scour.