The wide application of organic nanocrystals requires a deeper understanding of their nucleation mechanisms. In particular, the onset of nucleation still needs to be elucidated, although tremendous efforts have already been made in both experimental and simulation studies. In this research, we conduct molecular dynamics (MD) simulations, supported by quantum mechanical (DFT) calculations, to understand the mechanisms of the nucleation onset of organic perylene nanocrystals. Our DFT calculations indicate that face-to-face and face-to-edge molecular stacking can ultimately lead to the formation of a herringbone-style perylene nanocrystal. On the other hand, the results of MD simulations show the formation of clusters, which continues with the crystal nucleation in the form of unidirectional or multidirectional growth, depending on the feeding rate of perylene molecule in vacuum. This research helps to better understand the control of the growth of organic nanocrystals in modern nanotechnology.