Thin films of CsxTi(2−x/4)□x/4O4 (CsTiO), K4Nb6O17 (KNbO), and their proton-exchanged forms, i.e., HxTi(2−x/4)□x/4O4 (HTiO) and H4Nb6O17 (HNbO), were prepared using the electrophoretic deposition technique. The amine- and thiol-intercalated HTiO and HNbO films were prepared by exfoliation of powders in aqueous ethylamine and (mercaptoethyl)amine hydrochloride solutions, respectively. The heat-induced phase transformation of these films was investigated. Evidently, the CsTiO and thiol-intercalated HTiO films underwent phase transformation at relatively high temperatures due to the cations within the interlayer. CsTiO and HTiO films lost their layered structure and transformed, in turn, into the anatase and rutile phases with increasing temperature. However, the intercalated samples exhibited unidentified phases at in-between temperatures, eventually transforming to TiO2. The KNbO film transformed into a layered KNb3O8 structure, while the HNbO lost its layered structure completely to form Nb2O5. Thus, the phase change depended on the modification of the interlayers, and the heat treatment resulted in thin films with new crystal structures for the amine- and thiol-intercalated samples.