Natural halloysite nanotubes (HNTs) were employed as the support of Ru nanoparticles, and the corresponding activity was tested in an ammonia catalytic decomposition reaction for the production of COx-free hydrogen as the feed gas for proton exchange membrane fuel cell. N-2 physisorption, X-ray diffraction, Fourier transform infrared spectroscopy, transmission electron microscopy, hydrogen temperature-programmed reduction, and X-ray photoelectron spectroscopy were used to investigate the morphology and structure of HNTs and Ru/HNTs. The results show that HNTs possess a suitable specific surface area and pore volume, as well as a tubular structure with good thermal stability. The supported Ru nanoparticles are mostly located on the external surface of HNTs, whereas the interaction is weak between Ru particles and Si-O groups on the surface of HNTs. The dispersion of Ru particles decreases with the increase of the Ru loading content. The ammonia conversion increases with the Ru loading content from 0.3 to 5.6 wt %, and the turnover frequency of ammonia reaches a peak value at a Ru loading content of 1.1 wt %.