Powder bed fusion (PBF) process is expeditely moving towards its maturity for the direct manufacturing of intricated and sophisticated metallic parts. The typical process is instead complex and yet challenging to interpret experimentally. Modeling and simulation strategy has been widely implemented to comprehend and optimize the process. Therefore, an integrated simulation approach incorporating stochastic powder deposition and subsequently selective melting is developed to understand the consolidation mechanism in a multilayer process of electron beam PBF additive manufacturing. Simulation results of a thin-walled cross section are validated with the published experimental data to demonstrate the effectiveness of the proposed model. The simulation results of the multilayer process revealed that the layer thickness keeps on slight changes until reaching a steady state during the multilayer additive process. The stable powder layer thickness is systematically analyzed, which proved that the influence of the wall effect should be considered in smaller nominal layer thickness and denser powder bed. Finally, the printing quality in the multilayer process is dependent on adequate inter- and intra-layer bonding when the layer thickness reaches its maximum value, where agglomeration and balling effect in melt pool dynamics predominant by surface tension play crucial roles.