In this study, a periodic three-dimensional (3D) Ag/TiO2 nanocomposite architecture of nanowires was fabricated on a flexible substrate to enhance the plasmonic photocatalytic activity of the composite. Layer-by-layer nanofabrication based on nanoimprint lithography, vertical e-beam evaporation, nanotransfer, and nanowelding was applied in a new method to create different 3D Ag/TiO2 nanocomposite architectures. The fabricated samples were characterized by scanning electron microscopy, transmission electron microscopy, focused ion-beam imaging, X-ray photoelectron spectrometry, and UV-visible spectroscopy. The experiment indicated that the 3D nanocomposite architectures could effectively enhance photocatalytic activity in the degradation of methylene blue solution under visible light irradiation. We believe that our method is efficient and stable, which could be applied to various fields, including photocatalysis, solar energy conversion, and biotechnology.