Electronic circular dichroism (ECD) spectroscopy is the preferred tool for studying organic chiral supramolecules. However, it is a great challenge to experimentally clarify the contributions to ECD spectra from molecular vibrational motions and the intermolecular interactions, key factors for an efficient system architecture design of chemical sensors, catalysts, or optoelectronics. Focusing on this issue, here, we perform theoretical studies on the vibrationally resolved absorption and ECD spectra of two one-dimensional bay-substituted chiral perylene diimides (PDIs) by employing the non-Markovian stochastic Schrodinger equation (NMSSE) with respect to the model Hamiltonian in the diabatic representation, which includes the intramolecular localized excited states (LEs), intermolecular change-transfer excited states (CTEs), and the vibronic couplings (VC) as well. Our calculated results exhibit that the theoretical spectra, with the inclusion of the VC effect, agree better with the experimental ones than those without this effect and that the difference between the traditional absorption spectra of the two baysubstituted PDIs is much less obvious than that in their ECD spectra, verifying that ECD spectroscopy is sensitive to the absolute configuration and conformation of chiral supramolecules. We further make a comparison among the pure electronic spectra of aggregates with different aggregate sizes calculated by the time-dependent density functional theory and the mixed exciton model with and without decoupling the LE and CTE states. It is shown that the hybridization between LE and CTE states results in the emergence of new peaks or troughs in the high-energy band and a significant deviation between the calculated ECD spectrum and that predicted by the exciton chirality rule. It is further shown that the ECD spectra of oligomers exhibit an odd−even alternation pattern with changes in aggregate size.