The impact of conformational change on the ground and excited states of seven perylene diimide (PDI)-based dimeric systems is examined by introducing longitudinal shift, transverse shift, and rotation of one monomer with respect to another. The minimum energy conformations are compared via an energy decomposition analysis. The heteroatom-substituted dimeric systems, such as B2 N2-embedded PDI, trans-thio-PDI (trans-S2-PDI), and N-PDI, show BN···π, C═S···π, and N···H interactions that survive over a longer range of longitudinal and transverse shifts. The excitonic coupling analysis reveals that both Coulomb- and CT-mediated couplings are crucial for understanding aggregate absorption spectra. While the Coulomb coupling exhibits a monotonic behavior with conformation changes, the CT component changes significantly with minor geometrical deviations. The interplay between the two couplings leads to J-type, H-type, and null aggregates, depending on the conformations of the dimers. The overall trend of both couplings is consistent across all systems, although they differ in magnitude. The trans-S2-PDI shows the strongest Coulomb and CT couplings, while it is weak in perylene and B2N2-PDI dimers. The resonant model for strongly coupled Frenkel excitonic (FE) and CT states successfully characterizes the single- and double-band nature of absorption spectra in dimers. In strong coupling regions, the dimers show blue-shifted single-band excitation to the upper FE state. In contrast, excitation to the lower FE and upper CT states produces a red-shifted two-band spectrum in the weakly coupled regions. The intensity of the CT band diminishes with the monomer separation. In most cases, the perpendicularly stacked structures show null-aggregate behavior with no spectral shift due to the absence of Coulomb and CT couplings. The exciton relaxation pathway of the heteroatom-substituted PDIs is found to be influenced by the presence of nπ* states between the FE and CT states.