Objective To investigate and analyze the health status of special service personnel in the naval strategic transformation period, and to analyze their two-week prevalence and the changing trends, so as to provide pertinent medical and health care. Methods A total of 761 navy special service personnel were selected for this study. The two-week prevalence rate and the severity of diseases were investigated by on-site questionnaire survey, with the data of naval special service personnel investigation as in 2004 used control. Results There were significant differences in the two-week prevalence rate and disease composition of naval special service personnel in different periods and different categories. The two-week prevalence rate of naval special service personnel in our study was significantly higher than that in 2004 naval special service personnel investigation (41.13%[313/761] vs 32.26%[349/1 082], P<0.01). The two-week prevalence rates of skeletal muscle system diseases and neurological diseases were significantly higher those that in 2004 (P<0.01), and the two-week prevalence rate of connective tissue disease in skin was lower than that in 2004 (P<0.01). Divers had the highest two-week prevalence (64.21%, 61/95), followed by submarine crew (41.12%, 213/518), and the lowest was the pilot (26.35%, 39/148). The two-week prevalence rates of skeletal muscle system diseases, nervous system diseases and ears, nose, ihroat and oral diseases of divers were higher. Conclusion The two-week prevalence rate of naval special service personnel is increased during the naval strategic transformation period. The morbidity of common and frequent diseases is decreased, while the morbidity of occupational-related diseases is increased. Divers have a high two-week prevalence rate, with a significant occupational relevance.