The complex environment of night flights poses unique challenges to flight training safety. During night flight training, pilots must not only master general flight techniques but also overcome the intricate factors associated with nighttime navigation. These distinctive challenges test not only pilots’ technical skills but also place high demands on their psychological and physiological states. This study analyzes and empirically investigates the cognitive behavioral differences between flight trainees and instructors during night flight training. Using functional near-infrared spectroscopy, it explores the modulating effects of night flight environments and flight experience on pilots’ cognitive neural activity, revealing dynamic patterns of activation in the prefrontal and parietal lobes during night flight training scenarios, as well as behavioral strategy differences among individuals with varying levels of flight experience. The analysis of operational behaviors in night flight training between trainees and instructors found that instructors exhibited significantly superior brain activation patterns in cognitive neural processes related to night flight compared to trainees, particularly in the frontal lobe regions. Instructors demonstrated greater adaptability in cognitive neural performance to task difficulty changes, showing more flexible resource allocation capabilities. Flight experience also influences the coordinated processing across the entire frontal lobe and the frontoparietal network. The findings provide references for enhancing pilots’ night flight adaptability and improving night flight safety management systems.