The hydrogen flux inhibition of Pd-Ru membranes under exposure to 1–10% NH3 at 673–773 K was investigated. The Pd-Ru membranes were characterized by XRD, SEM, XPS, and hydrogen permeation tests. The results show that when exposed to 1–10% NH3 at 723 K for 6 h, the hydrogen flux of Pd-Ru membranes sharply decreases by 15–33%, and the decline in hydrogen flux becomes more significant with increasing temperatures. After the removal of 1–10% NH3, 100% recovery of hydrogen flux is observed. XPS results show that nitrogenous species appear on the membrane surface after NH3 exposure, and the hydrogen flux inhibition may be related to the competitive adsorption of nitrogenous species. By comparing the hydrogen flux of Pd-Ru membranes exposed to 10% NH3 with 10% N2, it is indicated that the rapid decrease in hydrogen flux is due to the concentration polarization and competitive adsorption of nitrogenous species. The competitive adsorption effect is attenuated, while the concentration polarization effect becomes more pronounced with increasing temperature.