The ortho- or para-substituents of NH2 or N-alkyl-containing lone-pair electrons were found to change the energy levels and transition configurations of the highest occupied molecular orbital for some fluoroquinolone-based antibiotics (FQs) and can significantly influence the electronic structure, intermolecular hydrogen bonding, internal conversion, and fluorescence and intersystem crossing efficiencies of FQs in acetonitrile or aqueous solution after photo-excitation. These findings provide new insights that can help in the molecular design strategies to regulate the photophysical properties of photosensitive medicines, photodynamic therapy reagents, and energy conversion materials that contain similar aromatic carbonyl structures.