Substrate-mediated gene delivery is an emerging technology that enables spatial control of gene expression and localized delivery. This is of particular interest for siRNA where surface-based release can greatly impact the fields of stem-cell reprograming, wound healing, and medical device coatings in general. However, reports on the use of siRNA for substrate-mediated delivery are scarce and have suffered from low efficiency. Here, an alternative strategy is reported by designing self-assembled substrates that experience stimuli-responsive topological transformations. Specifically, a methodology is established to promote the molecular organization of lipid films having 3D-bicontinuous cubic, 2D-inverted hexagonal, or 1D-lamellar nanostructures encapsulating siRNA. In response to a compositional, temperature, or humidity stimulus, the nanostructures evolve from 1D-lamellar or 2D-hexagonal to 3D-cubic resulting in efficient siRNA release to human cell cultures. Grazing incidence X-ray diffraction reveals that film nanostructures are highly ordered and preferentially aligned. The results indicate that film structure substantially affects siRNA delivery, with the supported 3D-bicontinuous cubic phase yielding the most effective reduction of gene expression. Subsequent studies suggest this enhanced performance arises due to the ability of this phase to cross cell membranes, particularly those of endocytic compartments. This work underpins that nanostructure tuning is decisive to the performance of therapeutic films.