Human factors is one of the important factors affecting the sub-health of air traffic control (ATC). It is of great significance to study the mechanism of human factors on sub-health of air traffic control. On the basis of previous researches on the human factors risk of ATC safety, the hierarchical structure model of human risk index system for ATC sub-health was established by using the analytic hierarchy process (AHP). Then, the initial theoretical model of controller’s individual factors affecting ATC sub-health was established based on the human risk index system. Finally, according to the theoretical model, the structural equation model (SEM) of controller’s individual factors affecting ATC sub-health was constructed, and the model was checked and modified by AMOS 24.0 software. The model fitting results show that: There is no significant correlation between business skills and physiological condition. The standard correlation coefficient between psychological condition and physiological condition is 0.60, and the standard correlation coefficient between psychological condition and business skills is 0.40, and the influence is significant. The standard correlation coefficient between psychological condition and ATC sub-health is 0.31, and the influence is significant.