Supramolecular assembly of donor-acceptor complexes as the key component in organic functional nanomaterials is a promising approach for future electronic devices. One representative example of the donor-acceptor complexes is the naphthalene diimide-pyrene (NDI-Py) system, which shows fascinating photoelectric properties. Herein, the analysis of the π-π interactions between NDI and Py has been investigated using the DFT/M06-2X and reduced density gradient methods. According to the calculations, the attractive forces for the stabilization of the NDI-Py dimer are dependent on the rotation angles, which provide physical insight into the experimental data reported by Wilson and co-workers (Langmuir, 2011, 27, 6554). Our results not only provide computational evidence for the origin of the rotation in the crystal structure of the NDI-Py but also address the role of the charge-transfer attractions in the complexes.