Objective To investigate the effects of submarine environment on the comprehension, memory and job performance of submariners through a comparative study. Methods A cluster sampling method was used to select 141 submarine crew members from a submarine detachment, and 159 off-shore crew members from a submarine base were taken as the controls. The comprehension capability was examined with comprehension testing subscale of Wechsler adult intelligence scale-Chinese revised in the two groups, and the memory capability was examined with picture arrangement subscale of Wechsler memory scale-Chinese revised. The job performance was evaluated by hand coordination tester and finger flexity tester, and the results were compared between the two groups. Results Comprehension test showed that the comprehension ability of submariners with a more than 5 years service experience was significantly lower than that of off-shore counterparts (t=4.67, P<0.01). In hand coordination test, the out track times were significantly more in submariners with a 3-5 and more than 5 years service experience than those in off-shore counterparts (Z=-2.20, P<0.05; Z=-2.21, P<0.05). In finger flexity test, the out track times was significantly more in submariners with a 3-5 and more than 5 years service experience than those in off-shore counterparts (Z=-3.08, P<0.01; Z=-4.52, P<0.01). Conclusion Comprehension ability and job performance of submariners are lower than those of off-shore counterparts. Comprehension ability of submariners with a more than 5 years service experience is worse than that of off-shore counterparts. Job performance of submariners with a 3-5 or more than 5 years service experience is worse than that of off-shore counterpart. The submarine environment has no obvious influence on memory of submariners.