Pilots\' operation behavior in flight is associated with their mental state variables such as workload, situation awareness, stress, etc. The objective of this study was to investigate the dynamic process of mental workload for pilots who perform a risky flight task in simulated scenarios. Two empirical experiments were conducted to address this issue. In experiment one, 19 trainee pilots divided into high-risk and low-risk groups performed a target-search task in a low-altitude visual flight. The results showed a statistically significant interaction between groups and segments for heart rate variability (HRV). The same pattern of physiological results was replicated among participants in experiment two, in which 19 airline pilots completed an approach with low visibility. These findings highlighted the relationship between mental workload variation and risk-taking behavior, which could be considered in improving pilot selection and training to improve flight safety.