Objective To explore the variation tendency and influencing factors of the hospitalization costs and hospital day of soldiers in a navy hospital, so as to provide reference for the health resource allocation of military hospitals. Methods The data of 16 278 military patients who were hospitalized and treated from Jan. 2008 to Dec. 2016 were extracted from the military health system. The hospitalization costs and status, variation tendency and influencing factors of hospital stay were analyzed by descriptive analysis, Mann-Whitney U test and Kruskal-Wallis H test. Results The average age of admission was (28.33±13.40) years, and the hospitalization period showed a shortening trend, while the hospitalization costs showed an increasing trend during 2008-2016. The polytomous variables, including services, patient's condition, hospitalized times, hepatitis B surface antigen, hepatitis C antibody, human immunodeficiency virus (HIV) antibody, military appointment, age and outcomes, and the dichotomous variables, including severe condition, critical condition, ICU admission, special-grade nursing care, first-grade nursing care, allergies and operation, were the influencing factors of hospitalization expenses (P<0.05). The polytomous variables, including services, patient's condition, hospitalized times, HIV antibody, military appointment, age and outcomes, and the dichotomous variables, including gender, severe condition, critical condition, special-grade nursing care, first-grade nursing care and operation, were the influencing factors of hospitalization stay (P<0.05). Conclusion The decreasing hospitalization day of military patients and increasing hospitalization costs suggest that the medical technology and hospital management efficiency are continuously improving, but facing the pressure of increasing medical costs. From a cost-effective perspective, we should strengthen the graded referral and control hospitalization costs and length of hospital stay.