In this paper, we report on the functionalization of silicon nanostructured (NanoSi) surface with an organic layer of nitrilotriacetic acid (NTA) and its subsequent use as an affinity surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) interface for histidine-tagged peptide enrichment and mass spectrometry analysis. The NTA terminal groups are immobilized onto the NanoSi surface via very stable Si–C covalent bonds. The NTA-modified NanoSi (NTA-NanoSi) interface was characterized by contact angle measurements, Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The NTA-NanoSi interface has shown a good selectivity toward His-tagged peptide and permits its enrichment from an artificial mixture of both tagged and untagged peptides and its subsequent mass spectrometry detection with good signal/noise ratio.