In order to elucidate the hydrogen effect on the atomic configuration in the Ni-Nb-Zr glassy alloys, we measured Ni, Nb, and Zr K-edge XAFS spectra of the Ni-Nb-Zr glassy alloy films with two different chemical compositions, i.e., Ni₄₂Nb₂₈Zr₃₀ and Ni₃₆Nb₂₄Zr₄₀, and their hydrogen-charged ones, i.e., (Ni₄₂Nb₂₈Zr₃₀)_0.91H_0.09 and (Ni₃₆Nb₂₄Zr₄₀)_0.89H_0.11. The Fourier transforms of the XAFS oscillations of these samples clearly shows that there is a significant difference in the structural response between the Zr30at.% and the Zr40at.% alloys when hydrogen atoms are charged. The curve-fitting analysis indicates that the hydrogenation does not alter the local alignment around the three metal atoms for the Zr30at.% alloy, but for the Zr40at.% alloy; it elongates the inter-atomic distances of Zr-Zr, Zr-Nb and Nb-Ni. On the basis of the curve fitting analysis, we propose the distorted icosahedral Zr₅Ni₅Nb₃ cluster models. The XANES spectra at each (Ni, Zr and Nb) edge of (Ni₃₆Nb₂₄Zr₄₀)_0.89H_0.11 also present the distinct shape from the other samples. The pre-edge peak (shoulder) vanishes or weakens, suggesting the conversion of the electronic state of the metal ions owing to the hydrogenation. The post-edge energy region shows clear multi-scattering effects from hydrogen atoms by charging these.