The Au-doped magnetic silica nanotube (Au-MSNT) was fabricated by sol-gel transcription and its binding ability for proteins was carried out by TEM, FIF-IR, and confocal microscope. The nickel nanoparticles with 3.5 ± 1.0 nm are homogeneously deposited on the inner side of a silica nanotube (SNT) with 220 nm diameter. In addition, the Au-MSNT clearly revealed the Au nanoparticles, with 9.3 ± 2.0 nm diameter. The Au-MSNT carried out the binding ability for protein as a guest molecule. The Au-MSNT acted as a receptor for the selective molecular recognition of biomolecules, particularly proteins containing cysteine. On the other hand, ubiquitin, which has no cysteine groups, was not immobilized onto the Au-MSNT. These results indicate that the Au-MSNT is efficiently recognized by the cysteine-containing protein.