The relationship between molecular packing and charge transport properties in bidimensional crystalline aggregates of N,N′-ditridecylperylene-3,4,9,10-tetracarboxylic diimide (PTCDI-C13), a prototypical n-type semiconductor for organic electronics, was investigated by an integrated approach based on atomistic molecular dynamics (MD) and density functional theory simulations. Calculations were performed to assess the morphological and dynamical properties of 2D crystals and nanoaggregates resulting from a set of PTCDI-C13 putative structures, differing in the relative orientation of the π-core between adjacent molecules. MD simulations indicate the cofacial crystal as the thermodynamically most stable phase and suggest the likely occurrence of competing two-dimensional structures at typical conditions for the growth of organic thin-films. In particular, the two most relevant structures found can be related to the kinetic and thermodynamic control of PTCDI-C13 crystal growth, respectively. Moreover, electronic structure calculations indicate a strong dependence of charge transport properties on molecular aggregation in the 2D crystals. Our simulations provide information, at the atomistic level, on the morphology of 2D aggregates of PTCDI-C13 in experimental conditions and shed light on the relationship between material processing and resulting charge transport properties, with a potentially strong impact in the development of devices based on PTCDI-C13.