Nanoimprinting methods have been used widely to prepare various patterned or nanostructured thin films from inorganic or organic components. However, the accumulation of large functional aromatic groups in covalently crosslinked nanoimprints is challenging, due to the difficulty in controlling the fluidity and reactivity of the precursor films. In this work, nanoimprinting of naphthalimide-silica sol-gel films results in vertically oriented nanoporous structures consisting of covalently crosslinked UV-absorbing frameworks. The nanoimprinted films demonstrate potential as robust analytical substrates for laser desorption/ionization mass spectrometry (LDI-MS). The sol-gel polycondensation behavior of the precursors is examined using 29Si NMR spectroscopy to determine reaction conditions suitable for nanoimprinting. The inorganic-organic hybrid frameworks containing a high density of naphthalimide groups exhibit small volume shrinkage during the polycondensation reactions, which leads to desired nanoimprinting. Various bio-related compounds on the order of picomole to femtomole quantities are detectable by LDI-MS measurements using the nanoimprinted substrates. To improve their user-friendliness and signal intensity in LDI-MS analysis, the nanoimprinted substrates are patterned with surface-modified silica nanoparticles. The direct formation of surface nanostructures by nanoimprinting of functional organosilica films may open a new path to developing optically and electronically functional materials, thereby widening their utility.