The geometric configuration of the corrugated Whipple protective structure significantly influences their protective capability against hypervelocity impact. To optimize the performance of the corrugated Whipple protective structures under hypervelocity impact, an integrated optimization method combining the finite element method-smoothed particle hydrodynamics (FEM-SPH) coupled algorithm with orthogonal experimental design was proposed. A reliable numerical simulation model was constructed, and the z-axis momentum density was introduced as an evaluation factor for protective performance. The three geometric parameters of the corrugation, namely thickness, span, and angle, were systematically investigated for their protective effects on the shielding. Orthogonal test results indicated that the order of influence of these factors, in descending order of magnitude, is thickness, angle, and span. Further double-factor refined tests were conducted, and a quadratic polynomial model was developed to identify the optimal geometric parameters. The optimal configuration improved the protective performance by 33.72% compared to a flat plate. The study confirms that the optimized corrugated structure effectively promotes projectile fragmentation and debris cloud dispersion, facilitating three-dimensional redistribution of the momentum, thereby significantly enhancing protective performance of the shield. This research provides a theoretical basis and a parameter optimization pathway to the design of spacecraft protective structures.