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Epoxy nanocomposites are promising materials for industrial applications (i.e., aerospace, marine and automotive industry) due to their extraordinary mechanical and thermal properties. Here, the effect of hollow halloysite nanotubes (HNT) on an epoxy matrix (Ep) was the focus of the study. The structure and molecular mobility of the nanocomposites were investigated using a combination of X-ray scattering, calorimetry (differential (DSC) and fast scanning calorimetry (FSC)) and dielectric spectroscopy. Additionally, the effect of surface modification of HNT (polydopamine (PDA) and Fe(OH) 3 nanodots) was considered. For Ep/HNT, the glass transition temperature ( T g ) was decreased due to a nanoparticle-related decrease of the crosslinking density. For the modified system, Ep/m-HNT, the surface modification resulted in enhanced filler-matrix interactions leading to higher T g values than the pure epoxy in some cases. For Ep/m-HNT, the amount of interface formed between the nanoparticles and the matrix ranged from 5% to 15%. Through BDS measurements, localized fluctuations were detected as a β- and γ-relaxation, related to rotational fluctuations of phenyl rings and local reorientations of unreacted components. A combination of calorimetry and dielectric spectroscopy revealed a dynamic and structural heterogeneity of the matrix, as confirmed by two glassy dynamics in both systems, related to regions with different crosslinking densities.