Objective To investigate the incidence of functional gastrointestinal disorders (FGIDs) in navy officers and soldiers (OSs) in grass-root units, and analyze their correlation factors. Methods A total of 1931 navy OSs from different regions and different services involved in the present study were selected by a cluster sampling method. The samples were investigated with the Rome III adult functional gastrointestinal disease diagnostic questionnaire (Rome Ⅲ-DQ), and diagnosis was made according to Rome III classification and diagnostic standard of FGIDs, and then the correlation risk factors were analyzed. Results A total of 1882 valid questionnaires were retrieved with validity rate of 97.46%. The overall incidence of FGIDs in navy OSs was 26.62%. Among FGIDs, functional bloating bore the highest incidence (8.66%), followed by functional dyspepsia (6.91%), irritable bowel syndrome (5.79%), functional constipation (4.57%), while the incidence of functional biliary pain was the lowest (0.7%). Comparison between different groups showed that the incidence of FGIDs was higher in 26-35 years group (54.78%) than that in 16-25 and 36-45 years group ( 29.73% and 15.11%, respectively, P<0.05); it was higher in college and higher education group (36.88%) than in senior middle school group and junior middle school group (23.03% and 26.44%, respectively, P<0.05); and it was higher in those coming from southern region group (32.01%) than those from northern or central region group (23.26% and 26.31%, respectively, P<0.05). The incidence of FGIDs was lower in naval pilots (12.09%) than in seamen serving on surface warships, surface logistics ship and submarine (26.29%, 24.29% and 28.32%, respectively, P<0.05). The incidence of FGIDs was higher in smoker group (35.78%) than in non-smoker group (26.31%, P<0.05), and in drinker group (alcohol drinking 10-20g/d, 67.22%) than in light drinker (alcohol drinking <10g/d) and non-drinker group (9.03% and 9.37%, respectively, P<0.05). Conclusion The incidence of FGIDs in navy OSs of basic units is high, and the risk factors include age, education degree, regions of their nativity, services they are serving, smoking, and alcohol drinking.