Soil aggregates consist of sand, silt, and clay size particles. Many of the clay size particles in soils are clay minerals, which actively influence soil behavior. The properties of clay minerals may change significantly as soil particle size decreases to the nanoscale; however, little information is available about these properties for the Ultisols in China. In the present study, the clay mineral components and structural characteristics of four particle-size fractions (i.e., <2000, 450–2000, 100–450, and 25–100 nm) of two Ultisol samples (Ult-1 and Ult-2) were investigated using elemental analysis, X-ray diffraction, Fourier-transform infrared spectroscopy, and thermal analysis. The molar SiO2 to Al2O3 ratios were lower in the nanoscale particle-size fraction (25–100 nm) than in the 450–2000 and <2000 nm fractions. This indicates greater desilicification and allitization of the smaller Ultisol particles. Furthermore, the Fe oxide and Al oxide contents increased and reached a maximum level in the 25–100 nm fraction of the two Ultisols. Goethite was mainly found in the 100–450 nm and 25–100 nm fractions. The dominant clay minerals in the Ultisol 25–100 nm fraction were kaolinite and illite with a small amount of a hydroxy-interlayered mineral in Ult-1 and gibbsite in Ult-2. The kaolinite crystallinity decreased as particle size decreased. The low crystallinity of the kaolinite in the A horizon 25–100 nm fraction was attributed to a reduction in the thickness of coherent scattering domains, as well as to decreases in OH groups and the dimensions of octahedral AlO6 sheets. A determination of the chemical and mineralogic properties of the different size fractions of the Ultisols is important to understand the desilicification and Al and Fe oxide enrichment mechanisms during soil formation. The significance of these results can help to reveal the nanoscale transformations of clay minerals. Analysis of clay mineral compositions in nanoparticles can provide the additional data needed to understand the adsorption and mobility of nutrients and pollutants.