Top-down synthesized TiO2 nanowires are presented as an ideal solid matrix to analyze small biomolecules at a m/z of less than 500. The TiO2 nanowires were synthesized as arrays using a modified hydrothermal process directly on the surface of a Ti plate. Finally, the feasibility of the TiO2 nanowires in the anatase phase as a solid matrix. The crystal and electronic structures of the top-down TiO2 nanowires were analyzed at each step of the hydrothermal process, and the optimal TiO2 nanowires were identified by checking their performance toward the ionization of analytes in surface-assisted laser desorption/ionization time-of-flight (SALDI-TOF) mass spectrometry. Finally, the feasibility of the TiO2 nanowires in the anatase phase as a solid matrix for SALDI-TOF mass spectrometry was demonstrated using eight types of amino acids and peptides as model analytes.