Two dimensional (2D) and three dimensional (3D) microstructures of metal nanoparticledispersed amorphous silica (Si-O) prepared by chemical solution process were observed using high angle annular dark field STEM (HAADF-STEM). In this study, the nickel nanoparticles in Si-O matrix were precisely studied on the relationship between microstructure and hydrogen affinity of the particles at high temperature. Total surface area of the Ni nanoparticles in Si-O was evaluated from average particle size derived from the particle size distribution of 2D HAADF-STEM images of powders with different metal contents. Amount of reversively adsorbed hydrogen on the interface of the nanoparticles and Si-O matrix for the samples were calculated using these data. Evaluated amount of adsorbed hydrogen was linearly increased and corresponds with the experimentally obtained result when the nanoparticles ideally dispersed in Si-O matrix with lower Ni contents. From 3D HAADF-STEM images, agglomerated particles were located on the surface of the composites, which results in decreasing the amount of reversible adsorbed hydrogen. Thus, it is thought that the reversible adsorption site was located at the interface of the Si-O and Ni nanoparticles.