We propose an improved fragmentation scheme for the generalized energy-based fragmentation (GEBF) approach, which improves the accuracy of the GEBF approach in total energy calculations and intermolecular interactions. The main modification is to introduce some two-fragment-centered primitive subsystems, which are neglected in the previous GEBF implementation. Numerical calculations demonstrate that the present GEBF approach can provide more accurate ground-state energies and intermolecular interactions. The present GEBF approach with the M06-2X functional and the cc-pVTZ basis set are employed to investigate the structures and binding energies in two dimeric species, which are related to pseudopolymorphism of a phenyleneethynylene-based π-conjugated molecule. A comparison of the binding free energies in a dimeric species and its corresponding model without CH⋅⋅⋅F contacts reveal that the substitution of fluorine atoms weakens the binding of monomers in the dimeric species formed by intermolecular OH⋅⋅⋅O hydrogen bonds, but strengthens the binding in the dimer formed by the π–π stacking interaction. Therefore, the CH⋅⋅⋅F contacts in these two dimeric species are demonstrated to play a less significant role.