In many large-scale land reclamation projects, vacuum preloading combined with a prefabricated vertical drain (PVD) system has been utilized successfully to improve the slurry with extremely high water content. However, in the use of PVD systems for soft soil with high fine contents, a dense "soil column" forms around the drainage board, which dramatically impedes the drainage and compromises the improvement level. To understand the soil column formation mechanism, coupled computational fluid dynamics-discrete element method (CFD-DEM) and scale-up strategy were employed in this work to study microsized soil particle movements. The results showed that the soil particles driven by the fluid gradually clogged the PVD board filter and then piled up. Under vacuum preloading, seepage occurred in the soil column, causing vacuum pressure loss and reducing the drainage velocity. As the permeability of the micron-sized soil column is exponentially related to the particle size, the drainage velocity through the soil column with high fine content was low. With the development of the soil column, the drainage velocity decreased, slowing the subsequent soil column development, and changing the packing structure of the soil column. In addition, the vacuum pressure, opening size of the drainage board filter, and cohesion among soil particles influenced the soil column formation. The effects of these aspects are discussed in this work to provide ideas for improving the drainage efficiencies of PVD systems.