Ergonomic assessments for specialized vehicle cockpits are often costly, subjective, or fragmented. To address these issues, this study proposes and validates a quantifiable comprehensive evaluation method combining optical motion capture with simulation. The methodology uses motion capture to acquire accurate, dynamic operator posture data, which drives a digital human model in a virtual environment. A novel assessment framework then integrates the results from six ergonomic tools into a single, comprehensive score using a multi-criteria weighting model, overcoming the ‘information silo’ problem of traditional software. In a case study optimizing a flatbed transporter cockpit, the method guided a redesign that significantly improved the overall ergonomic score from 0.422 to 0.277. The effectiveness of the optimization was validated by a 40% increase in key control accessibility and a significant reduction in electromyography (EMG) signals in the neck, shoulder, and lumbar regions. This study provides an innovative, data-driven methodology for the objective design and evaluation of customized human–machine systems, demonstrating its utility in reducing physical strain and enhancing operator comfort, with broad applicability to other complex industrial environments.