Lumbar fixator has been widely used, which can stabilize the lumbar spine and improve the fusion outcomes, but also lead to many complications. The effects of the internal fixator on biomechanical properties of the fused lumbar spine have been widely concerned for many years. However, most studies only considered the static loads and did not consider the effect of the fixator on the properties of the human lumbar spine under whole-body vibration (WBV). The purpose of this study is to investigate how the fixation system affects the biomechanical characteristics of the lumbar spine, fusion outcomes, and complications under WBV based on the finite element analysis. A three-dimensional nonlinear osteoligamentous finite element model of the intact L1-sacrum spine with muscles was established. A 5-Hz, 40-N sinusoidal vertical load supplemented with a 400-N preload was applied at L1 to simulate the vibration of the human body. For the adjacent segments, the fixation system may increase the risk of the adjacent segment disease under WBV. For the fused segments, the fixation system may decrease the risk of subsidence and cage failure including fatigue failure under WBV. The fixation system may provide a more stable and suitable environment for vertebral cell growth under WBV and lead to better fusion outcomes. This study reveals insights into the effect of the fixation system on the vibration characteristics of the lumbar and provides new information on the fixation system, fusion outcomes, complications, clinical evaluation, and selection of fixation system.