N,N-dioctyl-3,4,9,10-perylene tetracarboxylic diimide (PTCDI-C8) has become one of the most promising organic semiconductors for organic field-effect transistors (OFETs), owing to its high charge mobility and conjugated π-electron structure. The controlled selfassembly growth and patterning of molecules greatly affect the electronic and optical functions of PTCDI-based devices; yet, the molecular-scale deposition mechanisms on patterned substrates remain poorly understood. In this study, large-scale molecular dynamics (MD) simulations were performed using LAMMPS to investigate, at the atomic scale, the vacuum deposition and crystallization of PTCDI-C8 molecules on patterned cylindrical gold (Au) electrodes on a SiO₂ substrate. Four Au cylinders (32.5 Å in diameter, 34.5 Å in height) were arranged with a 22.6 Å spacing period to reproduce the experimental electrode morphology. PTCDI-C8 molecules were released one at a time from 135 Å above the substrate every 200 ps with random positions and orientations under NVT conditions at 350 K; after 48 ns, 240 molecules had been deposited in the simulation box. The simulations reveal that PTCDI-C8 nucleates preferentially at the step edges of the electrode sidewalls: few molecules remain on the roughened top surfaces, while most adsorb upright on the sidewalls and grow laterally within the inter-electrode gaps in a step-edgeinduced manner. This selective growth is driven by strong π-π stacking, favorable PTCDI-C8/Au interactions at the sidewalls, and the geometric confinement imposed by the electrode spacing. The first upright layer forms by this template-driven nucleation; once flat-lying clusters exceed a critical size, they undergo a collective reorientation to form crystalline nuclei that seed the second layer. Interaction-energy analysis reveals different driving forces for the two layers: the PTCDIC8/lateral-Au interaction energy rises with deposition and saturates after about 150 molecules, marking completion of the first layer, whereas the interaction with the top Au surfaces stays low, confirming that surface roughness suppresses further deposition there. Thus, while the first layer grows template-driven by step-edge-induced nucleation, the second layer forms mainly through intermolecular interactions between the long alkyl chains rather than through the electrode itself. The synergistic effect of surface roughness, large sidewall area, and intermolecular alkyl-chain interactions thus accounts for the multilayered PTCDI-C8 crystalline films in the electrode gaps. These findings agree with experiments and provide design guidelines for inducing layers to control molecular crystallization toward highperformance organic semiconductor devices.