This paper addresses the emergency protection requirements for ejection seats under high-speed conditions and proposes a simulation technology integrating experimental testing, dynamic CFD simulations, and finite element analysis to evaluate occupant head and neck whiplash injuries. The study performs computational simulations of aerodynamic forces on the occupant’s head and HIC values under two specific flight speeds: 850 km/h and 1100 km/h. The results demonstrate that the simulated aerodynamic loads have a discrepancy of only 6.6% compared to experimental measurements, indicating sufficient accuracy for research purposes. The HIC simulation successfully replicated the occupant’s head motion and impact with the canopy during ejection, showing consistency with test data from flexible neck anthropomorphic test devices (ATDs). Notably, at 850 km/h, secondary impacts between the ATD head and headrest resulted in an HIC value of 313.7, which is 7% higher than the 1100 km/h scenario. Both HIC values remain below the aviation industry’s threshold of 700, thus satisfying flight safety requirements. The findings of this research provide a valuable reference for the design and development of high-speed aerodynamic protection systems in ejection seat applications.