In this work, a novel nanorod-structured organic–inorganic hybrid material namely nanorod-[SiO2-Pr-Im-SO3H][TFA] (N-[SPIS][TFA]) has been synthesized, and characterized by FT-IR, energy-dispersive X-ray spectroscopy, field emission scanning electron microscopy, thermal gravimetric analysis and X-ray diffraction analyses. Thereafter, it has been applied as an efficient, recyclable and dual-functional catalyst to promote the following organic transformations: (1) the preparation of (6-amino-1,3-dimethyluracil-5-yl)-(2-hydroxy-1,4-naphthoquinone-3-yl)methanes by the one-pot multi-component reaction of 6-amino-1,3-dimethyluracil, 2-hydroxy-1,4-naphthoquinone and arylaldehydes; and (2) the production of bis(6-amino-1,3-dimethyluracil-5-yl)methanes via the pseudo-three-component reaction of 6-amino-1,3-dimethyluracil (2 eq.) and arylaldehydes (1 eq.).