To reduce the commonly high Neck Injury Criterion (NIC) and upper neck extension moment in the assessment of whip test injuries, based on the LS-DYNA finite element model and physical test results of a certain car seat, the basic structure and dynamic response under rear collision were first analyzed. A multi-rigid body dynamic analysis model for the seat whiplash test was established using the Mathematical Dynamic Model (MADYMO) software. Then, through the analysis of injury mechanisms and sensitivity analysis of the main design parameters of the seat, the main geometric structural parameters in the seat structure were determined, and a numerical model was established based on this. Finally, using multi-objective optimization algorithms, a corresponding optimization plan for seat whiplash resistance performance was obtained. The results showed that by adjusting the position of the seat frame crossbeam and headrest, the consistency of the passenger’s head and lower neck movement was improved, reducing the NIC by 58.5%, and the upper neck extension moment met the highest performance limit.