Polysilsesquioxanes (PSQs) are promising materials for protective coatings due to the robust thermal, chemical, and mechanical stability of their siloxane (Si–O–Si) networks. In this study, thiol-modified PSQs were synthesized via a sol–gel reaction to integrate self-healing functionality into hard coatings. To examine the influence of surface energy on self-healing and viscoelastic behavior, two variants were compared: a thiol-functionalized PSQ (R-TS) and a fluorine-containing thiol-modified PSQ (R-FATS). The thiol groups were transformed into reversible disulfide bonds through a photochemical process mediated by a photobase generator. The R-FATS coating exhibited enhanced hydrophobicity, which was attributed to the reduced surface energy of fluorinated groups. This lowered surface energy promoted interfacial chain mobility, resulting in improved self-healing efficiency and distinct viscoelastic behavior compared to the non-fluorinated R-TS coating.