Optimal physical fitness is essential for military personnel to effectively meet their rigorous physical demands. This study aimed to investigate the effectiveness of a suspension training program on physical fitness, biomechanical risk factors for lower extremity injury, mental health, and work-related factors in Navy personnel. A total of 50 young men participated in a randomized controlled trial. The participants were randomly assigned to two groups (n = 25): the intervention group and the control group. The intervention group performed an eight-week suspension training session three times per week, while the control group maintained their daily duties. The primary outcome was physical performance. The secondary outcomes were determined biomechanical risk factors for lower extremity injuries, mental health, and work-related factors. The data were analyzed using the analysis of covariance (ANCOVA). Compared with the control group, the intervention group showed significant improvements in physical performance, biomechanical risk for lower extremity injuries, and work-related factors from baseline to follow-up (p ≤ 0.05). However, there was no improvement in mental health. Based on these findings, suspension training positively impacted physical fitness, reduced injury risk, and enhanced the work-related factors of Navy personnel. This study provides new insights for various related experts and military coaches because it is an easy-to-use and feasible method with minimal facilities.