Novel proton-conducting ZrO2-WO3-SiO2 nanofilms of various compositions and thicknesses (∼50 to ∼300 nm) have been prepared by anodizing of magnetron-sputtered Zr-W-Si alloys in 0.1 mol dm−3 phosphoric acid electrolyte at 20°C. All the anodic oxide nanofilms examined reveal efficient proton conductivity after post-annealing at 250°C. Further increase in the post-annealing temperature results in the conductivity degradation for the anodic oxide nanofilms on the alloy containing only 5 at% silicon, while the high conductivity is maintained even after post-annealing at 300°C for those containing 15 at% or more silicon. The proton conductivity is dependent upon tungsten content; the conductivity of 5 × 10−6 S cm−1 for the ∼100 nm-thick films on the Zr31W55Si14 at 100°C is approximately 10 times that on the Zr48W37Si15. The anodic oxide nanofilms consist of two layers, comprising a thin outer ZrO2 layer and an inner ZrO2-WO3-SiO2 layer. Both layers show thickness-dependent conductivity and the proton conductivity of the two-layer anodic films is enhanced one order of magnitude by reducing the film thickness from ∼300 nm to ∼100 nm. Different mechanisms are proposed for the thickness dependence of the conductivity of the outer and inner layers.