The engineering of epitaxial, two-dimensional (2D) nano-heterostructures has stimulated great interest owing to an expectation of better functional properties (e.g., photocatalytic, piezoelectric). Hydrothermal topotactic epitaxy is one of the promising synthetic approaches for their preparation, particularly the formation of a highly ordered, epitaxial interface and possibilities for the preparation of anisotropic nanostructures of symmetrical materials. The present study highlights the key parameters when steering the alkaline, hydrothermal, topochemical conversion process from Bi4Ti3O12nanoplatelets to the intermediate, epitaxial, SrTiO3/Bi4Ti3O12nano-heterostructures and the final SrTiO3nanoplatelets by balancing the lattice mismatch and the supersaturation. An atomic-scale examination revealed the formation of an ordered epitaxial SrTiO3/Bi4Ti3O12interface with the presence of dislocations. The SrTiO3grows in islands for a stoichiometric amount of Sr (Sr/Ti = 1) and the growth resembles a layer-by-layer mode for surplus Sr content (Sr/Ti ≥ 12). The latter enables SrTiO3overgrowth of the Bi4Ti3O12basal surface planes, protecting them against dissolution from the top and consequently ensuring the preservation of the platelet morphology during the entire transformation process, the kinetics of which is controlled by the base concentration. A developed understanding of this particular transformation provides the guiding principles and ideas for designing other defined or complex epitaxial heterostructures and structures under low-temperature hydrothermal conditions.