Samples collected from the surface/subsurface of C-type asteroid 162173 Ryugu by the Hayabusa2 mission were nondestructively analyzed in three dimensions (3D). Seventy-three small particles (approximately 10–180 µm in size) were observed using X-ray nanotomography, with an effective spatial resolution of approximately 200 nm. Detailed descriptions of these samples in terms of mineralogy, petrology, and variations among particles were reported. The 57 most common particles consisted of a phyllosilicate matrix containing mineral grains, mainly magnetite, pyrrhotite, dolomite and apatite. The remaining particles were mostly monomineralic particles (pyrrhotite, dolomite, breunnerite, apatite, and Mg-Na phosphate) with two unique particles (calcite in a Al2Si2O5(OH)4 matrix, and CaCO3, phyllosilicate, and tochilinite-chronstedtite inclusions in a carbonaceous material matrix). The results confirmed that the samples correspond to Ivuna-type carbonaceous chondrites (CI chondrites) or related materials. Many small inclusions of voids and carbonaceous materials were detected in pyrrhotite, dolomite, breunnerite, and apatite. However, no fluid inclusions were observed, except for those in pyrrhotite that have already been reported. Magnetite exhibited a wide variety of morphologies, from irregular shapes (spherulites, framboids, plaquettes, and whiskers) to euhedral shapes (equants, rods, and cubes), along with transitional shapes. In contrast, the other minerals exhibit predominantly euhedral shapes (pyrrhotite: pseudo-hexagonal plates, dolomite: flattened rhombohedrons, breunnerite: largely flattened rhombohedrons, and apatite: hexagonal prisms) or aggregates of faceted crystals, except for Mg-Na phosphate. The matrices were heterogeneous with variable phyllosilicate particle sizes, Mg/Fe ratios, density (1.7 ± 0.2 g/cm3), nanoporosities (36 ± 9 %), and abundances of nanograins of Fe(-Ni) sulfides. The macroporosity of the particles was estimated as 12 ± 4 %. The observed textural relationships among the minerals suggest a precipitation sequence of: magnetite (spherulite → plaquette/framboid → rod/equant) → pyrrhotite (pentlandite → pyrrhotite) → apatite → dolomite → breunnerite → coarse phyllosilicates. Fe-bearing olivine (or low-Ca pyroxene) might have precipitated later than dolomite, indicating a high Mg activity in the aqueous solution. This precipitation sequence corresponds to a transition from irregular crystal forms (as seen in some magnetite) to regular forms of euhedral crystals (observed in some magnetite and other minerals). Based on the precipitation sequence and mineral morphologies, together with previously reported observations, a model for aqueous alteration in the Ryugu parent body was proposed as follows: CO2-H2O ice, amorphous silicates (GEMS-like material), and some minerals (mostly metal, sulfides, and anhydrous silicates) accumulated to form the parent body of Ryugu. Amorphous silicates and Fe-Ni metal quickly dissolved into the melted ice to form a highly supersaturated aqueous solution. Poorly-crystalized phyllosilicate and spherulitic magnetite precipitated first, followed by plaquette/framboidal magnetites with decreasing degree of supersaturation due to precipitation. Pseudo-hexagonal pyrrhotite plates were formed by dissolution and reprecipitation under relatively low supersaturation. Subsequently, apatite, dolomite, and breunnerite precipitated in this order in response to decreasing supersaturation.