As high-speed vehicles become increasingly lightweight, the influence of passengers on the vehicle vibration system cannot be overlooked. In this paper, a 3D vehicle-seat-human body coupled dynamics model is established to comprehensively evaluate the ride comfort of high-speed vehicles. The model combines the passenger biomechanics with the carbody flexibility. This is often neglected in previous studies and only the carbody vibrations are considered. Applying the validated model, four types of ride comfort evaluation indices are calculated and compared at 250–400 km/h. Results show that the ride comfort of high-speed vehicles at different speeds is excellent when the carbody acceleration and Sperling indices are used. While the results are significantly different when the total equivalent weighted acceleration and annoyance rate indices based on human body vibrations are used. At full load and speed of 400 km/h, the passengers sitting near the windows at both ends of the carbody felt ‘slightly uncomfortable’ or ‘less comfortable’ with an annoyance rate of about 30%, which indicates that up to 30% of the passengers might find the vibrations intolerable. This study underscores the necessity of integrating human body vibrations and passenger subjective psychology into ride comfort assessments, which can provide theory references for the selection and optimization of evaluation indices for high-speed lightweight vehicles.