The development process of seepage erosion is complex, influenced by numerous factors, and disasters triggered by seepage erosion are frequent, posing serious threats to structural safety. To study the effects of various factors on seepage erosion under vibration, this paper employs a CFD-DEM coupled analysis method. Seepage erosion experiments on eight groups of gap-graded sand samples were conducted to investigate the effects of fine particle content, confining pressure, and hydraulic gradient on the seepage erosion process under vibration. The micro-responses of the gap-graded sand samples were analyzed based on the fine particle loss ratio and axial deformation. The results show that under vibration, the fine particle loss ratio is higher, and axial deformation is more significant. The vibration has an aggravating effect on the seepage erosion, with the greatest effect on the upper layer particles, while the middle layer particles are least affected. Higher fine particle content leads to greater fine particle loss and longer stabilization time, making it a significant factor affecting axial deformation. Greater confining pressure results in more fine particle loss and axial deformation, with confining pressure having a mitigating effect on vibration. In the development stage of seepage erosion, a larger hydraulic gradient results in a higher fine particle loss ratio, with the hydraulic gradient having the least effect on axial deformation.