A series of donor–acceptor–donor (D-A-D) type small molecule (SM) donors containing Pechmann dye analogues (N, S, O) are designed and their geometrical, optoelectronic, charge transport, and photovoltaic properties are investigated using density functional theory (DFT). The structural modification of the donor backbone has been performed via additional sp2-nitrogen heteroatom incorporation in the Pechmann analogue acceptor cores. The N-heteroatom containing SM donors are found to be more air-stable due to having relatively deeper HOMO/LUMO levels than their unsubstituted counterparts. The maximum computed open-circuit voltage (Voc) is 1.53 V for the N-heteroatom substituted O-Pechmann core based donor. The designed donors are expected to harvest photon energy efficiently as their simulated absorption spectra lie in the visible region (575–724 nm). The N-heteroatom incorporation plays a significant role in lowering the charge recombination rate (KCR) and increasing the charge separation rate (KCS) at the SM donor/PC61BM interface. The ratio of interfacial KCS and KCR is found to be improved by times after sp2-nitrogen substitution in the Pechmann analogue cores. The maximum predicted power conversion efficiencies (PCEs) using the Scharber diagram reach up to 9% for the S-analogue of the Pechmann dye core based donor. This study sheds light on promising SM donors based on Pechmann dye analogues with low interfacial charge recombination rates and high charge separation rates and also demonstrates the impact of structural modification of Pechmann dye analogue cores on air-stability and overall photovoltaic performance.