Molecular engineering is significantly important for developing electron donor and acceptor materials of active layers in organic photovoltaics (OPVs). The OPVs based on halogenated donors frequently produced high power conversion efficiencies. Here, based upon density functional theory calculations with optimally tuned range separation parameters and solid polarization effects, we studied the effects of donor halogenation on molecular geometries, electronic structures, excitation, and spectroscopic properties for FnZnPc (n = 0, 4, 8, 16) and Cl(n)SubPc (n = 0, 6) monomers and the complexes with C-60 as well as the photoinduced direct charge transfer (CT), exciton dissociation (ED), and charge recombination (CR) processes that were described by rate constants calculated using Marcus theory. The tiny differences of the molecular orbital energy gap, excitation, and spectroscopic properties of FnZnPc (n = 0, 4, 8, 16) and Cl(n)SubPc (n = 0, 6) monomers suggest that halogenation cannot effectively tune the electronic and optical gap but the significant decrease of molecular orbital energies support the idea that halogenation has a remarkable influence on the energy level alignment at heterojunction interfaces. The halogenation also enhances intermolecular binding energies between C-60 and donors and increases the CT excitation energies of donor/C-60 complexes, which are favorable for improving open circuit voltage. Furthermore, for FnZnPc/C-60 (n = 0, 4, 8, 16) and SubPc/C-60 (n = 0, 6) complexes, the CR rates dramatically decrease (several orders) with increasing number of halogen atoms (except for F16ZnPc/C-60), meaning suppression of CR processes by halogenation. As for the special case of F16ZnPc/C-60, it underlines the importance of fluorination degree in molecular design of donor materials. This study provides a theoretical understanding of the halogenation effects of donors in OPVs and may be helpful in molecular design for electron donor materials.