To ensure the functional properties of an organ generated by the process of decellularization and recellularization, the initial density and distribution of seeding cells in the parenchymal space should be maximized. However, achieving a uniform distribution of cells across the entire organ is not straightforward because of vessel occlusion. This study assessed vessel occlusion during recellularization under different conditions. A combination of the electrical analog permeability (EPA) model, computational fluid dynamics (CFD), and discrete element method (DEM) was employed to describe the vessel occlusion phenomenon. In particular, realistic flow distributions in vascular trees of the decellularized organ were indicated by the EPA model. The cell suspension flow was modeled by a coupled CFD-DEM model, whereby living cells were presented as a discrete phase (solved by the DEM solver), and the culture medium was modeled as the fluid phase (solved by CFD solver). The cell suspension velocity was reduced up to 47% after decellularization, which directly affected cell movement. Simulation results also indicate that the occurrence of vessel occlusion was promoted by gravity direction in the asymmetric bifurcation and increased as the cell concentration increased. The assessment of vessel occlusion under different conditions was quantitatively investigated. The model provides insights into the dynamics of cells in the vessel compartment, allowing for the selection of optimum seeding parameters for the recellularization process.