Detection of leaks of flammable methane (CH4) gas in a timely manner can mitigate health, safety, and environmental risks. Zinc oxide (ZnO), a polar semiconductor with controllable surface defects, is a promising material for gas sensing. In this study, Ag-Ru co-doped into self-assembled ZnO nanorod arrays (ZnO NRs) was prepared by a one-step hydrothermal method. The Ag-Ru co-doped sample shows a good hydrophobic property as a result of its particular microstructure, which results in high humidity resistance. In addition, oxygen vacancy density significantly increased after Ag-Ru co-doping. Density functional theory (DFT) calculations revealed an exceptionally high charge density accumulated at the Ru sites and the formation of a localized strong electric field, which provides additional energy for the CH4 reaction with •O2- at the surface at room temperature. Optimized AgRu0.025-ZnO demonstrated an outstanding CH4 sensing performance, with a limit of detection (LOD) as low as 2.24 ppm under free-heat and free-light conditions. These findings suggest that introducing defects into the ZnO lattice, such as oxygen vacancies and localized ions, offers a promising approach to improving the gas sensing performance.