Previous studies have indicated a possible association between low back pain and intervertebral disc degeneration with prolonged exposure to vibration. However, the specific effects of different vibration frequencies under vertical sinusoidal excitation on the mechanisms of lumbar spine injury in seated individuals have not been clearly elucidated. Firstly, a validated whole-body finite element model was applied to perform modal analysis to investigate the modes that have a greater impact on lumbar spine vibration. Subsequently, employing transient dynamic analysis, it computed the time-domain responses of lumbar spine displacement, acceleration, stress, and pressure under sinusoidal excitation at different frequencies (1, 2, 3, …, and 8 Hz) in seated individuals. Finally, risk factors were applied to assess the impact of vibration frequencies on the lumbar spine. The modal analysis results indicated that the mode at 5.1 Hz significantly affected the vertical vibration of the lumbar spine. The time-domain response results showed that, compared to other frequencies, the intervertebral disc displacement, acceleration, stress, and pressure were larger under a 5 Hz vibration load. Risk factor assessments indicated that whole-body vibration near 5 Hz has a more adverse effect on the spine. It can be concluded that vertical vibrations close to 5 Hz can cause more damage to the lumbar spine than vibrations at other frequencies, increasing the risk of lumbar spine diseases. Therefore, appropriate measures should be taken to reduce or avoid the adverse effects of long-term exposure to whole-body vibrations at resonant frequencies on the health of the lumbar spine.