Functional gastrointestinal disorders (FGIDs) are common among the aircrew due to their arduous working environment. This study investigated the prevalence of FGIDs in Chinese male pilots and assessed the effects of trigger factors on the FGIDs. A cross-sectional study including 212 male pilots was performed in a Chinese large civil airline company. FGIDs were diagnosed according to the Rome IV diagnostic criteria. The psychological performance, dietary pattern, sleep situation, and physical activity of the respondents were assessed. Logistic regression analysis and structural equation modeling were used to explore the association between these trigger factors and FGIDs. FGIDs were observed in 83 (39.22%) respondents, of which 31 (37.35%) had overlap syndromes. Age, flight level, flight time, high-salt food pattern, anxiety, and sleep performance were found to be associated with FGIDs (all P < 0.05). Stepwise logistic regression analysis revealed that the flight level (OR 0.59, 95% CI 0.31-0.080), high-salt food pattern (OR 2.31, 95% CI 1.28-4.16), and sleep performance (OR 2.39, 95% CI 1.11-5.14) were the influencing factors associated with FGIDs. Structural equation modeling confirmed the correlations between FGIDs and the occupational, dietary, and psychological factors with a reasonable fit. The preventive strategies were necessitated according to occupational and psychological characteristics.