A series of beta-cyclodextrin (beta CD) amphiphilic derivatives with varying degrees of substitution were prepared by acylating beta CDs on their secondary face using thermolysin to catalyze the transesterification. After dissolution in acetone, the beta CD-C-n derivatives (n = 8, 10, 12, 14) were nanoprecipitated in water, where they self-organized into structured particles that were characterized using cryo-transmission electron microscopy (cryo-TEM) images and small-angle X-ray scattering (SAXS) data. Two types of morphologies and ultrastructures were observed depending on the total degree of substitution (TDS) of the parent derivative. The molecules with TDS < 5 formed nanospheres with a multilamellar organization, whereas those with TDS > 5 self-assembled into barrel-like (n = 8, 10, 12) or more tortuous (n = 14) particles with a columnar inverse hexagonal structure. In particular, faceted beta CD-C-14 particles (TDS = 7) appeared to be composed of several domains with different orientations that were separated by sharp interfaces. Ultrastructural models were proposed on the basis of cryo-TEM images and the analysis of the contrast distribution in different projections of the lattice. Complementary compression isotherm experiments carried out at the air water interface also suggested that differences in the molecular conformation of the series of derivatives existed depending on whether TDS was lower or higher than 5.